Category: hydroponic agriculture

A recent analysis of pit latrines concluded that globally, pit latrines accounted for 1% of anthropogenic CH4 emissions. The relatively large contribution of pit latrines to global CH4 sources can be attributed to the global extent of pit latrine use e approximately one-quarter of the global population e as well as the wet and unventilated conditions that drive anaerobic CH4 production. EcoSan relies on aerobic conditions to treat waste and has the potential to considerably reduce the GHG footprint of waste management. In aerobic thermophilic composting, CH4 emissions are typically low because of the presence of oxygen. However, anaerobic microsites created by uneven distribution of water in pores and hot spots of labile carbon can create conditions leading to CH4 emissions. The use of bulking agents and pile turning can be used to reduce the occurrence of anaerobic CH4-producing conditions and, when effective, carbon emissions from composting are in the form of CO2, which is considered to be climate-neutral because of its biogenic origin. Composting can, however, produce biogeochemical conditions prime for N2O emissions through nitrification or denitrification, including large sources of reactive nitrogen, dynamic and spatially varying levels of oxygen, and labile carbon sources. Quantifying the magnitude and balance of CH4 and N2O emissions in a given sanitation system is critical as the two gases have 100-year global warming potential values of 34 and 298, respectively. EcoSan systems utilizing aerobic, thermophilic composting are promising because they may mitigate GHG emissions from the waste and agricultural sectors, however these emissions reductions have not yet been quantified. Further, measurements of GHG emissions from management of solid organic wastes are especially limited from tropical climates , vertical farm system where implementation of EcoSan solutions are likely to be greatest.

To our knowledge, no direct measurements of GHG emissions exist from EcoSan systems that deploy container-based toilets and thermophilic composting of human excrement. Our primary objective was to characterize and quantify the GHG emissions resulting from the aerobic composting of human waste in EcoSan settings. We considered two operations that employed similar compost practices, but differed in the physical infrastructure that could alter biogeochemical conditions mediating GHG dynamics. We also compared the GHG footprint of EcoSan with alternative waste management pathways present in the region, including waste stabilization ponds and unmanaged disposal on grass fields. Finally, we undertook an investigation of the effects of compost management options that help reduce EcoSan GHG emissions.Greenhouse gas fluxes were measured from three sanitation pathways in Haiti: two waste stabilization ponds, two EcoSan operations, and a grass field where the illegal disposal of sewage was observed. The waste stabilization ponds were located in Croix ed Bouquets near Port-au-Prince, Haiti and operated by the Haitian government agency, Direction Nationale de l’Eau Potable et de l’Assannissement. Ponds consisted of uncovered concrete basins with effluent pipes connected to secondary overflow ponds. Two ponds were included in the sampling: a pond that received mostly septic tank waste , and another that received mostly pit latrine waste. Solid sludge was scraped out occasionally and stockpiled on-site. Solid and liquid waste from septic tanks and pit latrines were transported to the site and emptied into the waste stabilization ponds. The waste stabilization ponds represent the primary pathway of centralized waste treatment as advanced municipal wastewater treatment technologies are not present in the country. The EcoSan compost facilities were located in Port-au-Prince, Haiti and Cap Haiti€ en, Haiti. The sites received approximately 65 MT yr 1 and 440 MT yr 1 of human waste, respectively. Eighteen and 54 L container-based toilets were collected from households and communities, respectively, in each of the regions. Container-based toilets separated urine and feces into different compartments.Urine was disposed of on-site, and only solid material was transported to the compost facilities. Both facilities used a similar aerobic composting process consisting of a static thermophilic stage, followed by pile turning and maturation in windrows.

At the Cap-Haiti€ en operation, hereafter referred to as “Compost CH,” the ground was lined with cement to prevent leaching and an aluminum roof covered the area. Roofs and cement-lined floors were absent at the Port-au-Prince EcoSan operation, hereafter referred to as “Compost PAP”. During the initial thermophilic stage, approximately 2700 kg of fresh material from container-based toilets was added to a ~27 m3 bin consisting of air-permeable walls and an open top. Coarsely ground sugarcane bagasse was used as a bulking agent to create interstitial air spaces within the pile and as a 15 cm deep covering material. The material remained in the bin for about two months or until confirmation of Eschericia coli elimination, during which time it underwent static, thermophilic composting, reaching a peak minimum temperature of 50 C for at least 7 days. Following the thermophilic stage, the material was removed from the bin onto a flat surface, formed into windrows and aerated by weekly manual turning for two to three months. Finally, matured compost was then sieved and bagged for use as a composted soil amendment. The third waste disposal pathway was an unmanaged grass field near Quartier Moren, Haiti. Unregulated emptying of septic and pit latrine waste is not uncommon and has been observed here for at least five years and within a few months of sampling. While the frequency and magnitude of waste disposal in the grass field was unknown, there was apparent build up of organic material that resembled a moist, viscous sludge several inches to feet deep.Greenhouse gases were measured once at each site within seven days in July 2014. Fluxes of CO2, CH4, and N2O were measured using vented static flux chambers constructed of 25.4 cm diameter Schedule 80 PVC collars and chamber tops. 1.5 m tall collars were placed carefully in the semi-solid sludge in the waste stabilization ponds,vertical indoor farming approximately 1 m from the edge.Four areas were sampled in Pond 1, and six areas were sampled in Pond 2. Gas samples collected within ponds were treated as replicates and used to determine mean fluxes from each pond. Six 0.3 m tall collars were placed randomly in the Grass Field and allowed to settle for 1 h before the chamber tops were connected. Gas measurements were also made within and across compost piles of different stages. While sampling was conducted at each site at one time point, compost piles exist along a gradient of ages from freshly collected waste to mature compost. This design allows us to effectively substituting space for time to determine mean flux from each EcoSan system over the entire composting process.

At Compost PAP, eight piles ranging from <1, 1, 2, 4, 6, 8, 10, and 13 months were sampled, with six static flux chambers randomly placed in each pile. At Compost CH, six piles ranging from <1, 3, 4, 5, and 12 months old were sampled, with three static flux chambers randomly placed in each pile. Linear interpolation between age classes was used to calculate the net GHG emissions from EcoSan compost operations. Mean GHG emissions were determined by weighting fluxes by age of the pile. Gas samples were collected from the static flux chamber head space at 0, 5, 10, 20, and 30- minute intervals, immediately transferred to evacuated 20-mL Wheat on glass vials outfitted with 1-inch butyl septa. Samples were transported to the Cary Institute of Ecosystem Science in Millbrook, New York for analysis on a gas chromatograph. Methane concentrations were analyzed using a flame ionization detector. An electron capture detector was used to analyze N2O concentration, and CO2 concentrations were analyzed using a thermal capture detector. Samples with concentrations exceeding the maximum detection limit on the gas chromatograph were diluted at 1:10 or 1:100 with N2. Fluxes were calculated using an iterative exponential curve- fitting approach.To explore how compost management impacts GHG emissions, we established an additional experiment at the Compost CH site in August 2016. First, to test the effects of pile lining permeability, we measured GHG emissions using the procedure described above from a bin with a soil floor and from a bin with a cement floor and a blocked PVC overflow pipe , which were filled at approximately the same time. Second, to test the effects of pile turning, we measured GHG emissions one and three days after unlined bin material was turned for the first time, and compared emissions to those before turning. Twelve fluxes spaced evenly on a four x three grid were measured for each bin in the first stage to explore spatial variability of GHG emissions within the pile.

Six fluxes were measured per pile in the second turned stage, spaced on a three x two grid. The grid design also allowed us to explore the effects of pile structure and geometry on GHG emissions in greater detail.One-way analyses of variance followed by TukeyKramer means comparison tests were used to identify statistically significant effects of waste treatment pathway on mean CO2, CH4, and N2O fluxes. Treatment fluxes sampled across waste pathways were calculated as the mean and standard error of replicate samples collected within each system. Standard errors were propagated when considering mean GHG fluxes throughout the entire compost process at the EcoSan sites. For the compost management experiments, fluxes are represented as the mean and standard error of sample replicates. Fluxes of each gas species were considered separately and in combination using units of CO2-equivalents, using the 100-year global warming potential of 298 for N2O and 34 for CH4. Gas flux data were log-transformed to meet assumptions for ANOVA. Data are reported either as mean values±one standard error. Statistical significance was determined as P < 0.05 unless otherwise noted.We found pile lining permeability and pile turning significantly altered GHG emissions during EcoSan composting. A permeable soil lining lowered GHG emissions with pile CH4 and N2O emissions four and three-fold lower, respectively, in the unlined pile compared to the cement lined pile. Emissions also followed spatial patterns within the piles with CH4 emissions generally increasing from corners and edges to the center of the pile, with the opposite trend observed for N2O. Finally, substantial changes were observed in all GHGs after pile turning: CO2 and N2O emissions approximately doubled while CH4 emissions dropped almost to zero.We found that composting human fecal matter resulted in significantly lower overall GHG emissions than those observed from waste stabilization ponds and the illegal disposal of human waste on unmanaged grass fields. In EcoSan systems, CO2 was a major constituent of the overall GHG footprint, making up 42e62% of net CO2-eq emissions. In contrast, CO2 made up only 12% from grass fields used for dumping of untreated waste and 4e9% of the net CO2-eq emissions from waste stabilization ponds, suggesting that the ponds are not completely anaerobic. The difference in CO2 loss is likely driven by differences in oxygen availability among the waste treatment pathways. Composting systems enhance aerobic conditions that stimulate the microbial oxidation of organic carbon to CO2 , whereas biological treatment systems with oxygen-depleted conditions stimulate methanogenesis and production of CH4. Carbon dioxide produced from the decomposition of human waste is of biogenic origin, and therefore not considered a net source of GHG emissions from a climate change perspective. Conditions that evenly aerated compost piles, such as forced aerated and pile turning, tend to maximize CO2 production relative to CH4 and N2O. However, compost piles tend to have high levels of bio-geochemical heterogeneity due to within pile spatial variations in organic compounds, physical size and structure of material, oxygen diffusivity, density, porosity, and moisture content. Therefore, compost pile management can play a strong role in altering biogeochemical conditions that effect the composition of GHG fluxes. In the two EcoSan systems that we studied, we saw significantly higher CH4 fluxes from Compost CH, where static piles sat atop a concrete floor during the thermophilic phase. The presence of the floor likely built up moisture in the pile and increased the probability of anaerobic microsites. Methane emissions from Compost CH rapidly declined after the first two to three months, when piles were moved into the actively turned stage. In contrast, compost piles at Compost PAP were constructed atop compacted soil and without a roof covering, allowing for infiltration of leachate and higher rates of evaporation.

The original proportion of amorphous and crystalline cellulose before and after milling and 30–50% of sample crystallinity was lost after milling cotton for 15 minutes.Based on 1D CP solid state NMR measurements around 40% of crystallinity was lost and the initial crystallinity of the sample accounted for some inherent amorphous cellulose compared to x-ray scattering techniques.When pure cotton cellulose was milled crystalline cellulose fibrils showed loss in crystallinity and a consistent increase in amorphous cellulose, supporting mechanical preprocessing could induce recalcitrance.To test the current mechanical induced recalcitrance hypothesis in mechanical preprocessing, sorghum stems were subjected to lab scale vibratory ball-milling.In this study, stem tissue was used for initial experiments to allow for the highest concentration of secondary plant cell wall to increase the likelihood of observing recalcitrance with the greatest signal-to-noise ratio possible for solid-state NMR.Monitoring changes in sample morphology of the cellulose fibrils by FE-SEM is necessary because milling times vary depending on the biomass, sample quantity, and desired particle size.The time points include milling for 2 minutes at 30 Hz as common initial mechanical preprocessing time consistently executed for biomass18 and 15 minutes of milling at the same frequency to emulate longer milling times.Contrasting the effects of milling pure cellulose and milling cellulose in the plant cell wall also informed the selection of the 15-minute milling time point.Molecular changes in secondary plant cell wall polymers are probed with an initial set of solid state NMR experiments.The rINEPT was expected to selectively probe the highly dynamic polymers, lignin, and hemicellulose.

The CP-rINADEQUATE 66 probes directly bonded carbons in rigid components such as cellulose of the cellulose fibril and hemicellulose associated to cellulose fibrils.The CP-PDSD experiments were used to monitor the atomic cellulose morphologies using through space carbon-carbon correlations.Molecular recalcitrance markers include mobility and contacts of the dominant polymers by solid-state NMR experiments for polymers lignin, hemicellulose,vertical lettuce tower and cellulose.Monitoring markers of recalcitrance can be subdivided into each type of polymer.During the milling process crystalline cellulose is expected to convert to amorphous cellulose according to previous work on pure cellulose fibril structures of cotton by 1D NMR, FE-SEM, and vibrational spectroscopy.The resulting conformation change to amorphous cellulose within the plant cell wall may result in decreased access to crystalline planes of cellulose necessary for enzyme digestion.Assuming sample matter is conserved and no digestion occurs, proportions of crystalline and amorphous cellulose content in cellulose fibrils can be reported by NMR.5 Unlike vibrational spectroscopy where there is high signal overlap and sample crystallinity indexes afforded by x-ray diffraction, NMR contains well separated signatures for amorphous and crystalline cellulose.Cellulose polymers on the dehydrated interior, center, and more hydrated interior cellulose polymers of the cellulose fibril have distinguished chemical shifts over the last 20 years of experiments and specifically identified for sorghum.24 In 2D solid-state NMR experiments plant cell wall polymers compromise over a third of biomass and most of the signals due to the 13C labeling technique.When examining the plant cell wall in the spectra the carbon neutral region of polys accharides and lignin is 120–60 ppm and 170–110 ppm, respectively.Tracking proportional intensity changes of amorphous and crystalline cellulose distinguished by their chemical environments is possible.

Cross Polarized NMR experiments will select for the rigid polymers as the experiments are able to spectroscopically separate the rigid portions of the plant cell wall including the cellulose fibrils.CP based solid-state NMR experiments are more efficient for spins stagnant in spacepolymers of the plant cell wall.Cellulose fibrils are solid structures which can be probed with CP based solid-state NMR.Hemicellulose rigidly associated to cellulose in cellulose-hemicellulose interactions would also be selected for using CP experiments.In the context of the plant cell wall, cellulosehemicellulose interactions do vary based on the morphology of cellulose,so recalcitrance could also occur by additional amorphous cellulose-hemicellulose interactions common in grasses such as sorghum.Hemicellulose signals would then increase in their rigid signal intensity according to CP experiments and decrease in signal intensity from the highly dynamic signals.The highly dynamic signals captured in the rINEPT include 1H-13C correlations in the 2-D experiment and lignin with the plant cell wall.Lignin reorganization could cause recalcitrance in a variety of ways.One observable way would be cross-linkages forming due to mechanical activation ligninarabinose-xylan.The ether signals within lignin branching and lignin-hemicellulose cross-linkages are captured within the rINEPT experiment.Lignin condensation, aggregation, and cross linking noted in recalcitrance means highly dynamic lignin content is lowered , resulting in an expected decrease in signal intensity in the rINEPT.Digestible hemicellulose and cellulose would be reduced as polys accharides are trapped as lignin condenses in the secondary plant cell wall.Based on previous 13C evident methods and solid-state NMR analysis, the molecular evaluation of secondary plant cell wall architecture is feasible for bio-product relevant crops such as sorghum.This research project aims to identify where recalcitrance occurs in the deconstruction pathway and identify markers of recalcitrance using 2D solid-state NMR.The first step of the deconstruction pathway is investigated for mechanically induced recalcitrance for 13C labeled sorghum.How the heterogeneous secondary plant cell wall changes from preprocessing needs to be carefully approached.This work primarily focuses on intensity changes of unambiguous signals within the established sorghum native plant cell wall to circumvent misassignment of polysaccharide non-ambiguous peak changes which shift to ambiguous, overlapped chemical shifts during deconstruction.

Gao et al.2020 is used as a reference for secondary plant cell wall polymer chemical shift assignments confirmed in sorghum from previous literature which relied on extracted polymers,computational verification,and previous solid-state NMR9,on the architecture of the plant cell walls.Additional structural information can be confirmed from chemical shifts using computation, allowing for polymer morphological changes to be assessed based on changes in monomer orientation.Future work using data collected in this work could offer greater insight into polymer morphology changes.Given the heterogeneity of the plant cell wall samples,vertical grow rack system examining the recalcitrant markers would narrow the relevant chemical shift and chemical shift changes by computation as well as contrast chemical shifts of extracted polymers.Chemical shifts can support changes in polymer environments when peaks are well dispersed and unambiguous within a 0.5 ppm.For example, accessible polymers are expected to be more hydrated and have chemical shifts downfield.As cellulose fibrils are broken down into more disperse micro-fibrils or cellulose substructures, as discussed in Figure 2C, the chemical shifts of amorphous and crystalline cellulose may be expected to move downfield.Additional hemicellulose-cellulose association on hydrophilic surfaces of cellulose polymers would have chemical shifts potentially shift upfield for both polysaccharides.Upon the hemicellulose crosslinking to lignin may also result in chemical shift changes downfield for hemicellulose due to deshielding from bonding with the conjugated heteroaromatic lignin.However, recalcitrant organization of lignin trapping hemicellulose and cellulose in self-aggregation would reduce surface water may have chemical shifts moderately upfield compared to the expected literature values in sorghum based on Gao et al.2020 assignments of the secondary plant cell wall.These are generally anticipated chemical shift changes in polymers which is somewhat challenging given signal overlap of polysaccharides.In this work changes in chemical shift after mechanical preprocessing are highlighted by 2D integration of chemical shifts found in the control.Integration allows for minor changes or gradual changes in the plant cell wall to be assessed, increasing the ease of interpreting reasonable chemical shift changes upon preprocessing.Sorghum was grown hydroponically and then transferred to a growth chamber for carbon dioxide 13C labeling until they reached 16 weeks by collaborators Yu Gao and Jenny Mortimer as described in Gao et al.2020.The sorghum was incorporated with 92% 13C according to elemental analysis and are physiologically normal organisms.Upon harvest, the plants were flash frozen in liquid nitrogen, divided by tissue type , and cryogenically stored for later studies.

Samples were transported on dry ice between labs and stored at −80 °C for the duration of the study.Cut stems were milled using a Retch MM400 in a 10 mL zirconium grinding jar with two 10 mm zirconium beads at 30 Hz.For the 2-minute milling time point, 600 mg of cut stems were milled for a single 2-minute interval.For the 15 minute milling period, 600 mg of cut stems were milled in cycles for 5 minutes followed by 5 minute resting periods in accordance to relevant lab scale milling procedures from previous literature.After the milling period, the samples were divided into several cryogen vials and flash frozen in liquid nitrogen before storage in the −80 °C freezer.Sample Morphology Tracked with FE-SEM FE-SEM was employed to check sample morphology, specifically cellulose fibril morphology structures after milling.A Hitachi S-4100 T Scanning Electron Microscope was used to collect high resolution images for the control and milled samples using a procedure detailed in Zheng et al.2020.98 A 10 nm gold coating was sputter coated onto control and milled sorghum samples with a Cressington 208hr Sputter Coater.FE-SEM images were collected at a working distance of 15–6 mm with acceleration voltages ranging from 2–10 kV to achieve optimal spectra resolution.Atomic Resolution of Sorghum Stem Secondary Plant Cell Wall by MAS-ssNMR NMR experiments were performed on a Bruker 500 Solids NMR Spectrometer , with a Bruker 4 mm MAS probe and at a MAS speed of 10 kHz at the UC Davis NMR Facility.All samples were shimmed using a water sample file on the instrument.Two channels were utilized on the 500 MHz instrument, one was set to SFO2 500.0305 MHz for the proton and the other was set to 125.7445782 MHz for 13C.Spinal 64 1H decoupling was used.Decoupling powers were optimized for 1H radio frequencies of 71 kHz.The radio frequency power for CP on the carbon for the 1D and 2D NMR was a matched between protons and carbons at the 10 kHz MAS spinning frequency.32 Optimization of the 1H and 13C RF pulse lengths for each sample were obtained by locating nulls a carbonyl signal around 100 ppm in a 1D CP experiment with 4 scans with parameters similar to the 1D CP in Table 1.An 1-13C L-alanine sample was used to check instrumentation and calibrate chemical shifts on the TMS scale using a 1D CP experiment prior to data collection on the plant samples.99 Beyond these commonalities, parameters for the experiments applied to all the control and milled samples are summarized in Table 1.Samples were packed into 4 mm zirconium rotors with two 2 mm Teflon discs cut from Teflon tubing on the top and bottom to center the 13C sample.All data collection occurred at room temperature.Experiments on control stems revealed the total time of sample viability in the spectrometer to be approximately 52 hours and this was tracked for all experiments by periodic the collection of 1D CP and DP spectra for all sample data collections.The 2D was collection is divided into two sets of experiment collection per experiment as summarized in Table 1 and added together in NMR pipe for processing.NMR data were processed in NMRpipe with Gaussian line broadening applied before the Fourier Transform.100 Spectra were plotted in Sparky101 and formatted in Corel Draw 2019.A quantitative 1D DP experiment was employed to properly scale data on the milled and control samples for integration.Parameters of the quantitative 30 s 1D DP experiments were like 1D-DP experiment in Table 1 but the recycle delay was adjusted to 30 second recycle delay to assess the 13C content within the control and the milled stem samples.After data collection samples were stored at −80 °C in their respective 4 mm rotors for later use in the 1D-DP to quantitatively scale the sample loading of the samples which varied in consistency.The 30 s 1D-DP allowed for integrations across all experiments for each sample to be scaled for sample load which varied due to the consistency variation in the cut and milled samples.Milled samples were flash frozen before NMR data collection without changes to the plant cell wall.Cut stems were thawed for 3.5 hours based on the appropriate milling time for DMSO gel swelled plant cell walls of grasses outlined for 600 mg of material in Kim and Ralph 2010.Experiments in Table 1 and a DP-rINADEQUATE show no detected changes.The DP-rINADEQUATE had the same experimental parameters outlined in the CP-rINADEQUATE summarized in Table 1 with the cross polarization removed and the 13C nuclei directly irradiated.This meant samples could be milled, flash froze, and rethawed for data collection.

The plain hosts shallow water tables, which, combined with negative climatic water balances, makes it prone to salt accumulation both in its deep sediments and in the surface of its low landscape sectors.Grasslands dominate in the South of the sedimentary plain, showing some areas with salt affected soils.Besides those areas also few coastal and swampy areas with saline-acid soils are found as well as large internal salt marshes elsewhere, among them the Pantanal in southern Brazil, one of the larger wetlands of the world.Overview of anthropic salinity problems—In general terms, no country in Latin America is completely free from salinization, and we will focus our analysis on human-induced salinization, mainly caused by irrigation, though not exclusively.Most of the secondary salinization occurs in irrigated areasin arid and semi-arid zones, where intensive agriculture is practiced.This process is mainly due to non-efficient water management, poor drainage conditions, and low irrigation water quality.Irrigation mode and extension as well as type of crops vary considerably within the region.Fruit and vegetable production are mostly irrigated.In some area’s extensive crops such as sugarcane, rice, cotton, maize, and wheat are partially grown under irrigation, using modern technologies.In others, irrigated areas are populated by small holder farmers who generate most of the locally consumed food.The ratio between these two ways of production varies among countries and regions within them but does not to appear to be related to soil salinization processes.Arid and semi-arid areas under full irrigation are common in Mexico, Peru, Chile, and Argentina.While irrigated production value exceeds that of rainfed agriculture in Mexico, Chile and Peru, the reverse occurs in Argentina.In most cases furrow and flooding irrigation systems are used, but sprinkler, micro-sprinkler or drip irrigation systems are being increasingly adopted.

Waters from various origins are used,vertical farming tower for sale from surface to ground waters, and quality ranges from good to bad.Irrigation in non-graded and uneven lands has led to low water use efficiencies and rising groundwater levels.Low efficiencies are additionally caused by non-lined water distribution ditches and poor drainage conditions.Besides the typical effects of salts , boron is an additional problem in several irrigation districts.The Brazilian semiarid region in the northeast of the country is one of the largest semiarid regions of the world.It features tropical climate conditions with variable rainfall associated with high temperatures during much of the year.The region is also characterized by shallow soils, low quality irrigation waters, lack of drainage and often shallow groundwater.Irrigation has improved the economy of the region through diversified cropping practices, stimulation of agroindustry and export of products, but has also led to large areas being degraded by salinization because of poor water quality and deficient or absent drainage schemes.In general, those degraded areas are left fallow so that agricultural production is moved to other areas.The return of vegetation of these deserted areas would initiate a slow reclamation process.In semiarid/subhumid zones, as in Colombia, Venezuela, Cuba, the Dominican Republic and in some of the other countries in the region, similar salinization processes have occurred where sugarcane, rice and othertropical crops are irrigated with waters of varied quality and drainage is poor or nonexistent.Further south, in the temperate area of Pampas region of Argentina, field crops are usually grown under rainfed conditions but are exposed to occasional drought events.Supplementary sprinkler irrigation allows farmers to increase and stabilize grain yields.Exchangeable sodium has increased sharply but no consistent impacts on soil physical degradation have been detected.Human-induced salinization has also developed in the above-mentioned Chaco-Pampas plain, mainly promoted by land use and land cover changes, by cropping or overgrazing.In the Chaco and Espinal regions in the North of this plain, deforestation and cultivation have altered the hydrologic balance, mainly because cropped areas present lower evapotranspiration rates.

The resultant water excess infiltrates and slowly causes the rise of deep groundwater tables that bring salts to the surface, thereby damaging crops and soils.This process of salinization is somewhat like the “dryland salinization” in Australia.The Southern part of this Chaco-Pampas is mostly devoted to field crops, but alkaline and to a lesser extent saline soils predominate in an area known as the “Flooding Pampa,” where livestock production activities prevail.There, intensive cattle grazing removes vegetation and high evapotranspiration causes salts from the water table to reach the soil surface in the summer.Subsequent rains leach the salts, but this man-made process affects the composition of the plant communities.A similar process has been observed in grazed salt wetlands.Research on salt affected soils was very active in the 1960–1980 period, when several countries experienced large agricultural development through investments in large irrigation schemes.Research on soil salinity research at that time was mainly applied and based on results published by the US Laboratory Staff.One consequence of such effort was the organization of regional and international conferences, such as those that took place in 1971 in Colombia and in Venezuela in 1983.However, advances in research and evaluation of salt-affected soils subsequently faded.In most irrigated areas attention was focused on the engineering aspects of irrigation infra-structures rather than on the installation of effective drainage systems and adequate preparation of irrigation fields at the farm-scale.This has led to problems of drainage, water logging,and salinization.More recently, the development of large and expensive irrigation schemes has diminished, whereas new irrigation developments have been for small local irrigation units, using nearby surface and groundwater resources but most often done without consideration of regional impacts.In some extreme cases, due to competition for alternative uses of scarcely available good-quality water resources, non-treated residual waters of urban and industrial origin are used for irrigation.This is valid for small irrigation units, mainly dedicated to production for local markets, but not for larger irrigation units.Research on soil, water, and crop management in saline areas in Brazil is concentrated in universities and research organisms in NE Brazil.

Approaches include the development of soil and water management strategies, appropriate cropping systems, the sustainable use of brackish waters, cultivation of halophytes and salt-tolerant crops, application of mineral and organic amendments, phytoremediation and plant/microorganism interactions.A specific concern is the mitigation of socio-economic impacts of soil salinity in agricultural lands, which translate into loss or reduction of crop yields, profit margins, increased unemployment, and reduction of commercial land value.Technologies are being developed to provide a source of income for impacted smallholder farmers to provide for water and food security.This include the desalination of brackish water and its use in an integrated production system involving reject brine for farm-raised fish and the use of fish-pond water to grow organic salt-tolerant vegetables and forage crops for small ruminants.Argentina has active research on soil, water and crop management and salt tolerance mechanisms.Technologies on salt affected soils of humid/ sub-humid areas are aimed mainly at increasing biomass productivity without altering soil properties.They include grazing management, afforestation, agro-hydrological management, plant introduction, among others.Salinization in semiarid deforested areas has been studied in the great Chaco area and is focusing on ways to mitigate soil and water quality degradation , such as by changing cropping systems.The use and management of native woody species for degraded and salinized areas is considered.The characterization, collection and multiplication of both native and introduced species, and their incorporation into breeding program are prominent activities.Traditional breeding efforts have produced new salt-tolerant forage plant cultivars, such as Epica INTA Peman ,hydroponic vertical farming and new breeding alternatives have been explored to increase salt tolerance in Melilotus albus.Research on Lotus species for alkaline and sodic soils has contributed to their expansion in the Flooding Pampa.Molecular components of signaling chains and salt tolerance mechanisms have been successfully incorporated into commercial crops, soybean for example.Research interest in the region on salinity-related agricultural aspects has gained new momentum in this century, mainly in Brazil, Mexico, Argentina and Chile.In addition to many publications, this is also reflected by recent national salinity conferences in Argentina and in Brazil.The First Latin American Salinity Symposium was held in Fortaleza, Brazil, in 2019.Books on regional salinity issues have been published in Spanish and in Portuguese , including a recent comprehensive book.The subcontinent is re-awakening to its saline perspective.Social impacts of this problem are being addressed, particularly because of food security issues.The process of salinization in irrigated areas is continuing, although in some cases drainage and improved irrigation technologies improved the situation noticeably.However, in many Latin-American regions soil salinization is still expanding.Deforestation has been extensive, and the consequences of these land use changes will further cause land degradation and affect the sustainability of its land and water resources.It is expected that the coming decade will provide more certain quantification of its increasing spatial extent, as FAO and various organizations from Latin American countries are on the way to develop a contemporary soil salinization map, following unified protocols.

Problems with salinity in the Netherlands mainly occur in the North Sea coastal regions.Fig.31 shows in blue colors areas either above or below sea level protected by dikes and in orange color areas below sea level not protected by dikes.The white areas along the coast, including islands in the north and southwest, are dunes in which fresh water floats on sea water.Throughout history, various aspects of salinity were recognized and dealt with, specifically causes of salinization and sodification leading to soil structure deterioration, desalinization and rehabilitation by de-sodification, and crop salt tolerance/intolerance.Originally, experience of water managers and farmers formed the basis in their decision-making.From 1850 onwards, traditional opinions gradually evolved into scientific understanding.First, these were mainly based on chemical analysis of soils, later combined with physico-chemical concepts, and more recently through inclusion of analyses of flow and transport processes and plant physiology.In the first half of the 20th century, salinization and sodification arose from both natural floods and wartime strategic inundations.In the aftermath of the large 1916 flood, plans were made for the Zuiderzee Works, resulting in completion of the Afsluitdijkin 1932, changing the former tidal and saline Zuiderzee in a freshwater environment.Behind this dam are now the freshwater Lakes IJssel and Marken, surrounded by a series of new polders with a total area of 165.000 ha.In other words, where formerly was the Zuiderzee are now two lakes and the Wieringer meer and Flevo polders.The two lakes serve as fresh water reservoirs for the northern provinces, including replenishment of water pumped for domestic use in the coastal dunes.The early salinity research in the Netherlands was linked to consequences of the major floods and the Zuiderzee Works.Much of this specific research was presented in Raats and includes pioneering studies by Dutch scientists through the later 1800s and into the first half of the 20th century.Specifically, attention was paid to acid sulfate soils, application of gypsum to remedy soil structural degradation, analysis of plant salt tolerance, planting of salt tolerant vegetation to reclaim lands below sea-level , and understanding seepage from saline open water into lower lying land.Immediately following the devastating February 1953 Storm flood, the Delta Plan was launched, aimed at preventing recurrence of damage from such rare, huge storms in the future.The plan included upgrading all dikes along the entire coastline and build a series of barriers in the Southwest to close off all tidal inlets , except the Western Scheldt.The original main aims were protection of life and property and reduction of costs of maintenance of dikes.A reduction of saline seepage into many polders on the islands in the Southwest would also have resulted.During the execution of the Delta Plan, pressure from environmentalists and fisherman ultimately led to drastic changes in the plans.While construction of a dam in the Eastern Scheldt had started already in 1960, it was not until 1979 that parliament approved a novel type of storm surge barrier, with gates that can be closed when necessary.This barrier was completed in 1986.Earlier, in 1974 it was decided to keep the planned fresh water Grevelingen Lake saline by means of a sluice in the dam, which was completed in 1978.Density stratified flows—Already in the 1950s W.H.Van der Molen noted the occurrence of high salinities in the North-East Flevo Polder at depths of 10–15 m in places where a highly permeable Pleistocene deposit reached the land surface.He speculated that these high salinities were probably due to convection currents caused by the small difference in density between the freshwater present in the soil and the supernatant seawater of the former Zuiderzee between 1600 and 1931 AD.

The addition of these constituents has shown to increase the exchangeable sodium percentage of the irrigated soils , thereby affecting soil structural stability.The effects and mechanisms of salinity and sodicity on plants and soils have been extensively investigated between the 1960s and1980s ; see also Sections 2 and 12.Unique to irrigation with TE is the combination of organic matter , particularly dissolved organic content , with high concentrations of sodium.Clay dispersion was found in many studies to be enhanced in the presence of DOC.They concluded that, when irrigating with water of a given salinity, ESP was augmented in soils with lower OM content because the exchange selectivity for Na+ in soils decreases as their OM content increases.However, it was shown that OM can be either a bonding or a dispersing agent, depending on the level of the ESP, the particular chemical properties of the OM constituents, and the degree of mechanical disturbance of the soil.In particular, dissolved OM was found to disperse soil clay particles in the presence of anionic constituents, high ESP, and mechanically disturbed soil , conditions that are typical following irrigation with TE.Tarchitzky et al.showed that the hydraulic conductivity of a soil leached with TE decreased sharply relative to the small decrease observed when the soil was leached with a similarly composed electrolyte solution, but lacking the DOC.This result was explained by the interaction of anionic OM with positively charged edge surfaces of 2:1 clay mineral particles, preventing the edge-to-face association of the particles involved in flocculation.Therefore, the organic fraction from TE,stacking flower pot tower particularly the dissolved fraction, is not always beneficial in regards to sodicity and soil structural stability.Such complexity of the relationships between OM and soil permeability properties were reviewed by Churchman et al..

Additionally, the amplitude of the impact on the water retention and the hydraulic conductivity functions was different at each depth, suggesting that long-term use of TE for irrigation will differentially affect zones in the soil profile, depending on soil properties, water quality, irrigation management, plant uptake, and climatic conditions.The changes in soil properties echo the fluxes of the main flow processes in the soil, and consequently, affect water and nutrient availability to plants.Sufficient concentrations of root zone oxygen are crucial for healthy plant behavior.Assouline and Narkis demonstrated that the changes in the hydraulic properties of TE-irrigated soil impact not only the soil water regime but also root zone aeration.Irrigation with TE additionally affects soil microbial activityand composition of the bacterial community.Soil aeration and oxygen diffusion rates are likely reduced because of increased input of organic substrates and concurrent changes in water retention properties associated with TE irrigation.The short duration of most funded research projects limits our knowledge with respect to long-term impacts of irrigation with TE.Most studies report no significant statistical differences between TE and local fresh water irrigation in terms of crop yields, with the exception of specific ion toxicity issues, for example as a result of high boron concentrations.Recent long-term studies in Israel have shown systematic decreases in yields of orchards planted on clayey soils drip-irrigated with TE.Following more than 10 years of consecutive TE irrigation, avocado and citrus yields dropped approximately 20–30% in comparison with yields resulting from irrigation with local FW.Mechanisms explaining the loss of productivity under TE irrigation are yet unknown and likely involve multi-faceted interactions between chemical, physical and biological soil characteristics affecting plant function.One way to promote the success of utilizing water resources of marginal quality is to adopt irrigation methods appropriate to local soil and climate conditions and to develop appropriate site-specific irrigation methods and fertigation management protocols.

Pressurized irrigation methods, and especially drip irrigation, currently globally under-utilized, are more efficient than traditional surface irrigation and can minimize environmental impacts and health risks.These advantages come at a cost in terms of infrastructure, knowledge, maintenance and potential vulnerability to crop failure or soil degradation.In contrast with the large body of knowledge related to the performance of irrigation methods with respect to efficiency and crop response, very little is known about the long-term effects of different irrigation methods using marginal water on soil health and ecological function.Evidence suggests that the extrapolation of knowledge gained from FW irrigation with the various methods to their long-term performance with marginal water is unreliable and that specific monitoring of below ground soil ecological and hydrologic responses for cases of TE irrigation are needed.Increasing utilization of TE from sources including municipal, industrial, mining, and irrigation drainage waters dictates a need to consider the multiple effects of various ions and DOC on chemical speciation in the soil solution and exchanger phase as a function of irrigation water composition, water movement and solute transport through the soil profile, and crop water uptake.Moreover, models need to address physical transport processes as well as geochemistry.Beyond this, the impacts of TE, which is typically high in Na, K, Mg and DOC, on infiltration and hydraulic conductivity of the soil must be understood and quantified.Current knowledge regarding water quality—soil characteristic relationships is mostly limited to chemical sodicity and salinity factors and largely uncertain relating to other parameters.Evaluation of the impacts of pH, SOM, texture, clay mineralogy, tillage, and irrigation methods, for example, depends for now on field experience.Refinement and further development of current approaches to understanding and managing TE irrigation water, including these additional factors, are therefore important challenges and opportunities.Along with the expansion of TE, large scale desalination of sea and brackish water is rapidly becoming feasible as desalination techniques advance and its costs are continuously and substantially reduced.

Desalinated water is becoming a competitive source for irrigation, especially for high-value, salt-sensitive cash crops.A study on banana irrigation demonstrated that application of DS water can result in a yield increase of approximately 20% for the same amount of allocated FW water or to a significant reduction of about 30% of the irrigation amount if the goal is to achieve a prescribed commercial yield.However, it has been shown also that there is a need to adapt special fertilization protocols to this mineral-free water.Desalination has obvious positive impacts on water resources and the environments including augmentation of availability of good quality water and increased quality of TE following its municipal use and recycling.But it also presents several negative impacts for the environment, mainly: brine disposal from desalination process, chemical additives used for antifouling and anticorrosivity; and high consumption of energy that may increase emission of greenhouse gases.Soil salinization is practically inevitable when low quality water is used for irrigation in dry areas.That said, the actual impact is dependent on the irrigation method, the vertical and spatial distribution of soil properties, topography, cultural practices, weather, and regional hydrological conditions.Techniques for improving the quality of available irrigation water by mixing water sources of different qualities have been considered and could be adapted to the irrigation method.The appropriate mixing ratio becomes an operational state variable depending on the specific soil properties, climate conditions, and crop characteristics of the system under interest.The projected intensification of irrigated agriculture in areas utilizing marginal quality water will undoubtedly affect pre-existing fragile environments and threaten the overall sustainability and functionality of these agro-ecosystems.The future challenge is to devise strategies that increase food production while simultaneously preserving soil ecological functionality, minimizing human health risks, and promoting sustainable use of our land and water resources for agricultural use.Some of the most critical knowledge gaps,ebb and flow that must be addressed for sustainable and environmentally-responsible intensive agriculture utilizing low or marginal quality irrigation water are:risks to public health, for example by antibiotic resistance induced by wastewater use, or to the long-term ecological functioning of the soil system;interactions between marginal quality water with biological and ecological components; andimpacts of future conditions such as climate extremes on agroecosystem sustainability.Climate change is likely to accelerate soil salinization, specifically because of the increased crop water requirements by elevated temperatures, through sea level rise and additionally driven by further limiting freshwater availability for irrigation.It was suggested by Szabolicsthat climatic changes can double the areal extent of saline soils.The global impact of the changing climate on land degradation was recently recognized by the Intergovernmental Panel on Climate Change in their report on Climate Change and Land , analyzing interactions and feedbacks between climate, land degradation and food security.The most important direct impacts of climate change on land degradation are the results of increasing temperatures, changing rainfall patterns, and intensification of rainfall.

Changes in evapotranspiration and rainfall regimes exacerbate soil salinization, in addition to the intrusion of sea water into coastal areas, both because of sea level rise and land subsidence by groundwater overdraft.Many important indirect linkages between land degradation and climate change occur by way of agriculture.Yield reduction by soil degradationmay trigger cropland expansion elsewhere, either into natural ecosystems, marginal arable lands or by intensification, with possible consequences for increasing land degradation.In addition, precipitation and temperature changes will trigger changes in land and crop management, such as changes in planting and harvest dates, type of crops, and type of cultivars.As pointed out earlier , much research has been done to understand how plants are affected by a particular stressor, for example, drought, salinity, heat, or waterlogging, but research on how plants are affected by several stressors simultaneously is limited.It is the latter which is more realistic within the context of climate change.Climate change is causing sea levels to rise worldwide, particularly in tropical and subtropical regions.Assessing the extent of salinization due to sea water intrusion at a global scale has remained challenging.Seawater intrusion in coastal areas is generally caused by increased tidal activity , increased groundwater extraction or land-use change, causing contamination of nearby freshwater aquifers.The Indus delta in Pakistan , the San Joaquin Valleyin California and coastal countries around the North Sea are clear examples of increased soil salinization by seawater intrusion.In Hopmans and Maurer potential regional-scale impacts of global climate change on sustainability of irrigated agriculture were examined, focusing on California’s western SJV.The modeling study analyzed potential changes in irrigation water demand and supply, and quantified impacts on cropping patterns, groundwater pumping and groundwater levels, soil salinity, and crop yields, based on General Circulation Model climate projections through 2100 and using three greenhouse gas emission scenarios.Crop water demand was expected to change very little, due to compensating effects of rising temperature on evaporative demand and crop growth rate.This simulation study projected that reductions in surface water supply are going to be offset by groundwater pumping and land fallowing, whereas soil salinity is expected to increase in down slope areas, thereby limiting crop production.The results also showed that technological adaptation, such as through improvements in irrigation efficiency, may partly mitigate these effects.Another recent computer modeling study for the Tunisian coastal region, simulated changes in coastal aquifer salinity and the associated increased groundwater pumping required to offset the increased irrigation requirements and soil salinity levels.Corwin evaluated various climate change impacts on soil salinity through analysis of various case studies in selected countries with different soil salinization processes with a focus on methods for monitoring soil salinity development.In addition to climate parameters affecting soil microbiological processes directly, specifically relevant as to their contribution to greenhouse gas emissions of CO2, N2O and methane by soil respiration and redox reactions, respectively, soil scientists are considering secondary soil salinity effects on soil microbiological processes.For example, Egamberdieva et al.reported reduced soil microbial biomass with increased soil salinity, comparing a wide range of salinity levels for field grown cotton in Uzbekistan where salinity has significantly increased after the expansion of irrigated agriculture in the 1960s.They suggested that the lower microbial population was caused by increased microbial stress by both osmotic and toxic effects.In a subsequent review article , the isolation of salt-tolerant plant growth promoting rhizobacteria from both saline and sodic soils evidenced that these could mitigate both biotic and abiotic stresses.It is suggested that selected rhizobacteria can be inoculated to reclaim saline agro-ecosystems, enhancing their productivity and soil fertility.Furthermore, it is proposed to prioritize gene-level studies of ST-PGPR, parallel to that of seeking salt-tolerant crop species.Similarly, Shrivastava and Kuman proposed that microorganisms could play a significant role toward soil salinity stress management, and pointed to the need to further exploit selected unique properties such as salt tolerance and other interactions with crop plants such as the production of plant growth promoting hormones and bio-control potential.In the last decade,many different genera of bacteria have shown to provide tolerance to host plants under different abiotic stress environments.

Rather than spectral reflectance, Ivushkin et al.used satellite thermography to assess soil salinity in salt-affected cropped areas in a semi-arid province of Uzbekistan.They found that correlations between soil salinity and canopy temperature varied depending on the time of year with the strongest relation occurring for cotton in September.The thermographic approach has also been applied to larger regional-and global-scales.Remote sensing of salinity has moved beyond proof-of-concept, but few salinity monitoring programs utilize satellite RS.One exception is the Land Monitor under the National Dryland Salinity Programin Australia, which tracks salinity in Western Australia.However, further research is needed to establish that RS is sufficiently accurate and cost effective for more general use.We recognize several priorities: Data integration—With satellite imagery, trade-offs exist among spatial, temporal, spectral, and radiometric resolutions.Satellites and instruments used for indirect remote salinity detection include Landsat 7 ETM+and Aqua/Terra MODIS.The most recent iterations of long-operating open satellite platforms offer improved imaging capabilities while commercial satellites such as WorldView-3 offer spatial resolutions approaching 1m.Research is needed to integrate data from these varied platforms and technologies because each potentially captures information important for salinity detection.High temporal resolution is important because spectral and thermal response varies according to phenological stage.High spatial resolution is important because salinity often varies substantially over very short distances.However, the finest possible resolution is not necessarily optimal, as correlation between remotely sensed data and soil properties may be highest at coarser resolutions.For instance, Scudiero et al.used data from the WorldView-2 satellite to examine salinity correlations in a 34ha fallow field and determined that the relationship between multi-temporal maximum EVI and soil salinity was strongest at a resolution of about 20m.

Future research should develop multi-spatial,aeroponic tower garden system multi-temporal, multi-sensor data analysis pipelines to improve accuracy.Crop-specific information—Research should prioritize regression and classifier models that integrate crop-specific data.As noted, spectral and thermal response to salinity stress differs by vegetation type and growth stage, but very few RS salinity models have used crop specific crop data.Exceptions include the work by Scudiero et al.who used the Cropland Data Layer to incorporate cropping statusin to their model, and Zhang et al.who explored the possibility of incorporating crop-specific reflectance properties in their regional salinity assessments.Future research should investigate the use of crop type and growth stage as predictor variables.Two crop categories that create difficulties for indirect remote sensing methods are salt-tolerant halophytes and orchards and vineyards.Halophytic vegetation complicates image analysis because in contrast to the monotonically decreasing salinity response function of most agronomic crops, halophytes achieve maximal growth at intermediate salinity levels.While most true halophytes have little agronomic value, there is growing interest in their use as bio-fuels.Orchards and vineyards are mostly excluded in salinity RS studies.For example, the salinity map of western San JoaquinValley produced by Scudiero et al.covered only row and field crops because insufficient information existed for orchards.Hyperspectral imagery—Multi-band vegetation indices have been the predominant measure of canopy reflectance in RS studies.However, hyperspectral imagery potentially provides a more informative measure of crop status as potentially 100s of wavelength bands can be analyzed simultaneously.Irrigating with water that is high in salt content requires special management practices to mitigate salinity buildup in the crop rooting zone, to minimize reduction in crop yield with associated economic losses and to mitigate environmental degradation.In addition, saline-sodic irrigation water can cause breakdown of soil aggregates, followed by the swelling and dispersion of clays particles which leads to soil crusting, loss of porosity and reduced permeability especially after rainfall or irrigation with low salinity.The degradation of alkali soils using high quality irrigation waters has been documented early on, resulting in reduction in soil infiltration.We will discuss the historical evolution of improved soil salinity management practices in irrigation projects, followed by changes in soil salinity management strategies that have occurred in the past few decades.

Early on with the development of irrigation projects, there was general recognition that soil salinity issues had to be addressed at both the on-farm scale and at the basin or irrigation district scale.On the farm scale the focus was on agronomic and engineering practices that minimized soil salinity buildup in the root zone, while at the basin or regional scale the focus was mostly on engineering structures for water delivery and drainage.In our review we will focus on the farm-scale only, though it is realized that with few exceptions soil salinity issues will persist when regional efforts to ensure adequate drainage facilities are lacking, and will eventually lead to the demise of civilizations and land abandonment.We also note that most irrigation projects were designed for surface irrigation by flooding the field using gravity , allowing for over-irrigation to ensure that the whole field receives adequate amounts of water while satisfying the annual leaching requirement.However, this has led to rising groundwater tables worldwide, further necessitating drainage capabilities.At the same time, these shallow groundwater tables can be beneficial when irrigation water supplies are limited such as in drought periods.A succinct review by Ayers et al.lists main criteria to assess whether in situ crop water use from shallow ground water is suitable.To prevent the buildup of salts in the root zone, agronomic recommendations would apply irrigation water in excess of crop evapotranspiration.The excess water was commonly referred to as the leaching requirement, maintaining a field salt balance with soil salinity levels to not exceed the crop salt tolerance.In situations when leaching was inadequate to prevent salt buildup in the root zone, salt tolerant crops were selected.Seedbed preparation by tillage and higher frequency irrigation were used for sodic soils to mitigate the effects of surface crusting and to promote stand establishment.However, tillage can reduce soil infiltration through formation of a plow layer.For that purpose, deep plowing is used to break the plow pan and to increase leaching and soil water storage in the deep rooting zone.Other soil salinity management strategies included sanding, by mixing clay layers with sand from further down below, thereby improving the effectiveness of leaching, or by creating artificial subsurface barriers.

Flood irrigation, though suited for irrigation with saline water because of its leaching benefit, is often associated with problems such as soil crusting and soil aeration.These are minimized using furrow irrigation, however, because of its partial wetting of the soil surface it tends to accumulate salts in the seedbed.For that purpose, annual preplant irrigations by flooding or sprinklers were applied to flush salts from the shallow root zone before or during seedling establishment.Chemical amendments are used to replace the excess exchangeable sodium with calciumin sodic soils to improve soil infiltration.In addition to gypsum, other amendments include calcium chloride, sulfur, and lime.Addition of such amendments is typically followed with a leaching irrigation to move Na and other reaction products downwards away from the rooting zone.Soil conditioners continue to be used for management of saline-sodic soils,dutch buckets for sale particularly at seedling establishment in high ESP soils or when crops are irrigated with high SAR water.Soil conditioners such as sulfate lignin were reported to improve soil aggregate stability and permeability and prevent crust formation.Also, organic manures are used to manage saline-sodic soils irrigated with lower quality water, as these promote soil aggregation and increase soil permeability.Organic manures arealso used to lower soil pH by releasing CO2 and organic acids as it decomposes, whereas the lower pH helps in solubilizing CaCO3 when present, thereby increasing soil EC and replacing the exchangeable Na with Ca which lowers ESP.In the last few decades, substantial changes have occurred in irrigation technology, irrigation water sources and cropping systems.Also, public awareness on environmental issues and their regulations have increased.Consequently, soil salinity management is changing as well.Leaching—Leaching remains an effective management strategy to prevent salt build in the root zone.However, more recent research is showing that soil salinity leaching requirements developed decades ago were based on steady state conditions and that the transient models developed later improved the prediction of the complex physiochemical-biological dynamics in an agricultural system.They concluded that the current guidelines overestimated leaching requirements , especially if LR are low.Most importantly, the salt concentration at a given depth is not constant with time as assumed by steady-state models, but is continually changing as water is added or extracted by the plant.Furthermore, under monsoonal conditions, rainwater mobilizes accumulated salts downwards and restores high quality soil water in the rooting zone during the growing season, thus further reducing the LR as computed by the steady state model.The concentrated salts near the soil surface are “flushed” by the irrigation water thereby moving the salts downwards and reducing the concentration at a given depth.

As a result, the concentration after irrigation near the soil surface would be close to the concentration of the irrigation water for high-frequency irrigation systems.Such findings indicated irrigation water amounts could be reduced and that more saline waters and marginal waters could potentially be used for irrigation.These results were affirmed by Corwin et al.and Corwin and Grattan.In addition, using both field experiments and transient numerical modeling studies, Hanson et al.showed that there is considerable localized leaching around drip systems, even at applied water volumes less than potential crop ET, as drip systems only partially wet the soil surface.Deficit irrigation —DI consists of application of irrigation water below potential crop requirements.DI strategies such as partial root zone drying and regulated DI are used to save water and increase water productivity but will increase soil salinity when annual LF values are less than one.In a 5-year field study on peach trees, Aragu€
es et al.determined that this increase was counteracted by salt leaching by high LFs attained during the non-irrigation seasons and proved to be sustainable for the climatic conditions of their study area.However, in a similar study using low-quality irrigation water they determined that long-term application of moderate saline waters would increase soil salinity in the long-term, unless unusual large volumes of irrigation water were applied in the non-irrigation season.Clearly, long-term outcomes of DI will largely depend on crop salt tolerance and climatic conditions.Crop selection—Selecting salt tolerance crops continues to be used as a simple strategy to deal with saline-sodic soils irrigated with low quality water.For example, in the western San Joaquin valley cotton production has been replaced by pistachio, which is both salt tolerant and a high value specialty crop.However, in general there are not that many crop choices that are both salt tolerant and high value as most fruit and vegetables tend to be salt sensitive, such as lettuce and strawberries.Boron and chloride ion toxicity on woody perennials is occurring more frequently as acreage of this crops is expanding in California.Typically, more water is needed to leach boron than other salts because it is tightly adsorbed on soil particles , whereas tolerances vary among species and root stocks.Boron concentrations in the irrigation water exceeding 0.5–0.75mg/L have been reported to reduce plant growth and yield.Unlike boron, chloride moves readily with the soil water, is taken up by the plant roots, translocates to the shoot, and accumulates in the leaves.If irrigation water that is high in chloride is applied via sprinkler irrigation it can cause foliar injury and reduce yields in hot climates.Options to reduce foliage injury include irrigation at night or early morning when evaporation rates are low and using infrequent and large irrigation applications.Effect of irrigation systems on soil salinity management—The soil salinity pattern that develops in the root zone is a function of the water distribution pattern of a given irrigation system.Over the last 2 decades, there has been a rapid conversion from surface irrigation to pressurized irrigation systems particularly drip irrigation in places like California.The rapid increase in adoption of drip irrigation has been driven by both the demonstrated ability to improve productivity and water use efficiency, as well as it is incentivized by governments.Surface irrigation systems remain the most widely used method of irrigation around the world.Recent advances in automation and real-time data analytics for surface irrigation have demonstrated improved water use efficiency in Australia and California.Distributing applied water more uniformly across the field results in leaching of salts with less water.But traditionally, surface irrigation systems such as flood have typically had lower leaching efficiencies than micro-irrigation systems, because under soil saturation large fractions of applied water move through macropores thereby bypassing the salts in the smaller pore spaces of the soil matrix and aggregates.However, automated gates and SCADA control systems can now allow flood irrigation systems to achieve leaching efficiencies like pressurized irrigation systems.

A distribution ratio value of one indicates that the rate of prey available in the capture zone is equal to that in the water above the sea anemone . A ratio greater than one indicates that more prey were swimming in the water above the sea anemone than were swimming in the water that passed through the sea anemone’s capture zone.Capture efficiency was defined as the proportion of encountered prey that was captured.Trapping efficiency was calculated rather than feeding efficiency because the duration of experiments was short relative to the average ingestion times for sea anemones , thus most captured and retained prey were not ingested during the videos. The duration of the experiments was chosen to minimize the chances that prey would show a decrease in swimming and escape behaviors . Using prey encountered as the denominator when calculating rates for both capture and trapping efficiencies enabled these efficiencies to be compared with published feeding efficiency data for a zooplanktivorous fish . In addition, these efficiencies could be directly related to ecological models that estimate suspension feeding rates from encounter rates. We found that increasing the “strength” of ambient water flow enhanced rates of some steps in the feeding process and decreased others for a passive suspension-feeding predator eating zooplanktonic prey that have strong escape responses. Encounter rates normalized to capture volume depend on the speed of the water moving through the capture zone,dutch bucket for tomatoes and on the turbulence of the flow that stirs the water carrying new prey into prey-depleted water in the capture zone. Therefore, we expected that higher peak wave velocities and turbulence would enhance encounter rates for sea anemones, and this effect was observed for dead copepods.

We also found that encounter rates were greater in strong waves than in weak waves for living copepods, but there was high variation in encounter rates for these swimming prey, thus the difference was not statistically significant. If the tentacles of a predator are deformed by hydrodynamic forces, the volume of the capture zone can be reduced as the velocity of ambient water increases , thereby reducing the rate of encounters in strong waves. However, such deformation of the capture zone did not occur for A. elegantissima in the flow regimes used in our experiments, and all rates were normalized to capture volume. In weak waves more copepods swam above rather than in the capture zone of the sea anemone, whereas in strong waves the copepods were evenly distributed vertically within the water column near the sea anemone. We expected that this difference in vertical distribution would further enhance encounter rates in strong waves compared with weak waves. However our results suggest the variability in the behavior of living copepods plays an important role in shaping encounter rates. We expected that capture rates would be higher for sea anemones feeding in strong waves than in weak waves. We observed that fewer of the copepods passing through the capture zone executed escape maneuvers that avoided the predators’ tentacles in strong waves than in weak waves. Similarly, Heidelberg et al. found that zooplankton could avoid or escape benthic suspension-feeding corals under conditions of slow flow. Likewise, Robinson et al. showed that in weak waves , copepods executed escape maneuvers that enabled them to avoid being captured by a siphon that simulated suction feeding by a predatory fish, whereas in strong waves , the copepods were unable to detect hydrodynamic cues of the siphon and did not swim to avoid capture. Thus, Robinson et al. found higher capture rates for their siphon in strong waves than in weak ones. In our study of A. elegantissima we also found that capture rates were 75% greater in strong waves than in weak waves, but this difference was not significant due to the high variability of encounter rates and the low capture rates of A. elegantissima .

Retention rates were the same for both conditions of flow , and represented less than 0.5% of the prey encountered by a sea anemone. In turbulent and wavy flow, hydrodynamic forces can sweep captured prey off the tentacles of the predator . In slow flow with low turbulence, fewer prey are encountered and captured per time, but a greater proportion of them are retained by the predator than in faster, more turbulent flow. The net result is that the rate of retention of prey of a passive suspension-feeding benthic predator did not change as wave peak velocities and turbulence increased. Nematocysts on the tentacles of sea anemones adhere to prey that contact the tentacles. The adhesive strength of the nematocysts of A. elegantissima was found to be independent of habitat, availability of food, exposure to light, and species of symbiont . This suggests that the lower retention of prey by A. elegantissima in strong waves was not due to physiological differences in the ability of tentacles to hold onto prey, but rather was due to higher hydrodynamic forces dislodging prey in the more rapid flow. Stronger waves increased feeding efficiency for benthic zooplanktivorous fish but had no effect on feeding efficiency for a passive suspension-feeding sea anemone . In both cases, the escape behavior of zooplanktonic prey in slow flow resulted in lower capture rates than in faster flow. As peak velocities and turbulence increased, fewer of the prey moving through the capture zone were stimulated to execute escape maneuvers in response to either type of predator. Although the fish reduced feeding effort and the time spent feeding during a wave cycle, their foraging efficiency improved in stronger waves. These active predators were able to modify their behavior in a way that minimized expenditure of energy for foraging in faster, more turbulent flow, yet their feeding rates increased because fewer of their prey tried to escape capture. In contrast, passive suspension feeders do not swim after their prey and thus probably expend less energy per prey captured than do darting fish. Passive A. elegantissima maintained the same trapping efficiency in both weak and strong waves because, although they capture more prey per unit time in stronger waves, they also lose more of the prey that they catch in the faster, more turbulent flow.

This study reveals the importance of both the behavior of the prey and the flow of ambient water in determining the predation rates of benthic predators. In slow water feeding rates on non-swimming or weakly swimming zooplanktonic prey might be higher than on prey with strong escape responses. Furthermore, studies of feeding by benthic predators on passive particles that have no swimming behavior might overestimate feeding rates. Likewise, feeding studies of shallow-water benthic predators carried out in flumes with steady-state water flow that does not mimic the waves and turbulence to which such predators are exposed in nature could yield unrealistic feeding rates because actively-swimming prey might be able to avoid predators more readily in steady flow with less turbulence and no back-and-forth flow of waves, and the ability of predators to hold on to captured prey exposed to steady drag forces might be different from their retention abilities when prey are exposed to the pulsatile hydrodynamic forces in turbulent waves. Predators capture prey in complex and variable environments. In the ocean, bottomed welling organisms are subjected to water currents, waves, and turbulent eddies. For benthic predators that feed on small animals carried in the water , flow not only delivers prey but can also shape predator-prey interactions.Turbulent flow can stir the fluid environment, enhance prey delivery ,blueberry grow pot reduce the ability of the prey to detect and avoid predation , or wash prey off capture surfaces . How does flow impact predator-prey interactions between a benthic suspension feeder and zooplanktonic prey? Studies of passive suspension feeding have been done experimentally in unidirectional flow for corals , bryozoans , sea pens , and sea anemones , but few studies have examined the effects of waves and turbulence on suspension feeding . Experiments have generally focused on the consumption of non-motile prey, yet actively swimming zooplankton can contribute significantly to the diet of passive suspension feeders . Brine shrimp neutrally-buoyant cysts, or hatched nauplii have been used as live prey . A small number of studies of benthic suspension-feeding predators that used zooplankton prey suggest prey swimming and escape responses might impact capture rates. Although Artemia spp. nauplii can swim, they do not exhibit escape behavior. Previous research on this ubiquitous feeding strategy has been useful in estimating how much suspension feeding can contribute to ecological links between pelagic and benthic communities. A common measure of interactions between predator and prey are encounter rates . For sedentary predators that rely on ambient water to deliver food, encounter rates are dependent on the ambient flow and prey behavior. Humphries suggested the efficiency of particle capture might be higher than estimated for filter feeders in low flow. Chapter 2 suggests that retention is not 100% as is often assumed, and can be a small fraction of the initial encounter rate . The presence of neighbors affects flow around benthic suspension feeders. Okamura found that the feeding rate of an encrusting bryozoan colony was enhanced in the presence of a neighboring colony. The feeding current from the upstream colony drew currents closer to the substratum so that downstream zooids captured more prey.

Passive suspension feeders do not generate their own feeding current. However, ambient flow over a bumpy surface of organisms can generate eddies from which extended tentacles can capture prey from turbulent wakes . The objective of this study was to measure how ambient water flow, prey swimming behavior, and the presence of neighbors affect predation by benthic passive suspension feeders. I addressed this question using sea anemones, Anthopleura elegantissima , which live in wave-dominated flow habitats , feed on a variety of zooplankton that exhibit different swimming behaviors, and live in dense colonies surrounded by conspecifics . In this study we used prey with different swimming behaviors: 1) the calanoid copepod Acartia spp., which has a well-characterized escape response , 2) heat-killed Acartia spp., which are non-swimming prey with the same size, shape, and drag as living Acartia spp., and 3) nauplius larvae of Artemia spp., which are swimming prey with no escape behavior. We examined the effects on feeding of the peak water velocities and turbulent kinetic energy of the wavy ambient water flow, prey swimming and escape maneuvers, and upstream and downstream neighbors. Understanding how zooplankton swimming and the effect of neighboring suspension feeders in realistic flow conditions can contribute to predictions about the link between pelagic and benthic communities based upon flow and prey type. All sea anemones, Anthopleura elegantissima, were collected in October 2012 and May 2013 from Horseshoe Cove, in the Bodega Marine Reserve along the Sonoma Coast in California . The clone from which sea anemones were selected was the same bed over which flow measurements were collected . Sea anemones that were next to one another and positioned away from the edges of the clone were selected. Since A. elegantissima forms genetically identical polyps by binary fission, adjacent sea anemones were likely from the same clone though genetic testing was not performed. Sea anemones were gently peeled from the rock, and each individual was placed in an air-filled plastic bag. The bags were transported to the University of California Berkeley in a cooler kept at 10-15°C. The anemones were housed in a 19-L aquarium filled with recirculating filteredsea water with a salinity of 35‰. The aquarium was kept in a temperature-controlled cold room at 10-15 °C and exposed to a photoregime with 12 hours dark and 12 hours light provided by full-spectrum fluorescent bulbs . The sea anemones were placed on a suspended plastic mesh substratum to prevent attachment to the aquarium walls, and were fed hatched Artemia spp. nauplii once a day, but were not fed 24 hours before use in flume experiments. For flume experiments, sea anemones were transported to the University of North Carolina Wilmington via overnight delivery. Individual sea anemones were placed in plastic bags that were filled with oxygen. The bags were packed into a Styrofoam cooler over a base of ice packs and a middle cushioning layer of newsprint. Upon arrival sea anemones were removed from the plastic bags and housed under aquarium conditions identical to those previously described.

The relation between islands as non spaces and designed places is a convoluted one, but it is a relation that must be kept in mind in the discussion that follows. I will take this section of the introduction to explain my use of the concept of design as it relates to the scientific and social construction of islands and the themes of visitation, vulnerability, and biocomplexity. As mentioned above, the phrase itself, “islands by design,” is the name of a Bahamian environmental assessment and design consultation firm whose projects have included the design plans and use concepts for large marinas and planned developments on several islands. Much like “living laboratory,” I have borrowed this idea and redefined it to suit my purposes. I also borrow here from the History of Science including the history of Anthropology, and I pick examples from Island Archeology, Island Ecology, Tourism Studies and Urban Studies to talk about the power of design and the way it can engender various forms of experience.A columnist in one of The Bahamas’ national papers stated in print in 2007 that, “planning is the key to sustainability,” and notions of design and planning were conspicuous throughout my work with field researchers, conservation managers, and government officials. Conservation and management organizations are currently going through the process of designing and developing science based management plans for everything from individual protected areas to national protected area master plans with guidance and design models from international conservation organizations and consultants; The design of scientific field research projects is often as important a product as the research results when it comes to forms of knowledge created by research scientists and students; Design for the curricula and scope of a new degree program in “Small Island Sustainability” at the College of The Bahamas is currently underway; The newly created Ministry of Environment is redesigning the roles of its own governmental institutions,u planting gutter becoming a central player in the planning processes for projected social and economic development in the country; the Department of Sustainable Tourism is redesigning the ways in which the islands of The Bahamas should be marketed to foreign visitors and reconceptualizing the form tourism infrastructure should take in various locations; The Ministry of Tourism is considering how to redesign its “tourism product” to not only mitigate and adapt to threats of climate change but to discover ways in which to profit from a newly climate aware target traveler.

This is to name only a few examples of the rootedness of design schemes in the Bahamian milieu. I note that design processes come prior to planning, that planning is an aspect of the enactment of thought and design, and the newspaper quote could more accurately say, “design is the key to sustainability.”“Design,” as a term, implies the creation of plan, an intention, a pattern, a contrivance, and productive work to “create the form or structure of something.” This last implication is one of the most important for me, in that I would like to make the creative and formative aspects of field science, sustainable development, and environmental management explicit. Islands by design, then, references the multiple ways in which nature and natures, life and lives, matter and materials, places, spaces, and objects, etc. become conceptually and aesthetically formed and reformed as part of the work of science-based environmental, touristic, and sustainable planning in The Bahamas. The point is not only that natural science and scientific expertise is touted as the position of authority from whence ecological problems can be diagnosed and framed in certain circles- the point is also that natural science and scientific expertise is in the position to influence and set the terms for how solutions will be studied, formed, and enacted. Experts, albeit a somewhat motley crew with disparate backgrounds when it comes to nationality, discipline, realm of experience and outlook, can be considered the designers of the living laboratory. I see the living laboratory as a site of great productivity in the development of the conditions of possibility. With the notion of islands by design, I am in essence proposing another direction for political ecology or environmental anthropology to take, or perhaps another set of tools to add to the rich set which this unruly sub-discipline already possesses. I think that focusing on and conceptualizing design is one way to attempt to describe the work, The study of scientific laboratories as special spaces for social production became a characteristic of the sociology of science beginning in the 1970’s. Ethnographers of science sought to decentralize the analytic focus on human agency through the study of lab practices with an attention to the ways non human substances have a “material agency” in the production of scientific facts.Latour and Woolgar’s Laboratory Life introduced readers to the daily lives of scientists involved in the construction of such facts. Famously using the trope of an anthropologist in the field attending to “science in the making” they noted that all new laboratory activity hinges on previously constructed and accepted facts embodied in lab instruments and that laboratories undergo continual “micro-processes” of negotiation in their operation as a system of fact construction.

The vast amount of literature, documents, and “material dictionaries” produced by labs become important as part of the fact making process and the material arrangements of the lab produce a reality that would not exist without it.They write, “It is not simply that phenomena depend on certain material instrumentation; rather, the phenomena are thoroughly constituted by the material setting of the laboratory.” The laboratory is therefore a space which embodies the work of other fields, reified in its arrangement and equipment, to legitimate the reality it produces; reality and nature are the byproducts of the scientific stabilization of facts in the lab, rather than the cause. In an important observation, Mol and Law note that laboratory experiments are “simplificatory devices: they seek to tame the many erratically changing variables that exist in the world, keeping some stable and excluding others from the argument.”Their point is that simplifications are used to justify action, yet they qualify this by stating that simplification should not be denounced off-hand as it is a productive force, especially when it comes to knowledge practices. As mentioned above, the notion of The Bahamas as a living laboratory for certain sciences and disciplines is a framing concept for this dissertation. The phrase itself, “living laboratory,” originated from an interview with a Bahamian government official who hoped that the international research community might increasingly come to see The Bahamas as a living laboratory for environmental research,planting gutter and it is a concept I have borrowed and stretched to fit my own interests. This can be differentiated from Harre’s use of the term “living laboratory” to describe how living things become crucial aspects of scientific laboratory experiments.For Harre, living things are transformed, in the space of the lab, into instruments and apparatus for measurement, detection, simulation, and experimentation. An important part of the lab “has always been organic, apparatus and instruments constructed from living materials or materials that were once alive.” He provides the example of the fly, Drosophilia, and genetics research: the fly became a piece of lab equipment in that it was a means of producing specific kinds of knowledge as a standardized organism in a system of production; the fly was a designed artifact. Harre writes, “glass must be skillfully blown to become a flask.So too the living material must beshaped and transformed into devices in the living instrumarium.”

It is this experimentation with living things that he calls the living laboratory and he thus uses the phrase in a slightly different valence and for different purposes. My use of the term is also about living things, but as I will show below, it is about the production and manipulation of ideas framing life and living as much as it is about the scientific use of living things in The Bahamas today. His focus is on animal bodies and individuated organisms, while mine is on the way in which processes and systems are identified and designed as sites for experiments or environmental management and the way these “natural” processes are conceptually linked to other enterprises. Following Latour and Woolgar, but taking them into the living laboratory of The Bahamas, this dissertation starts from the point that nature and its scientific forms, i.e. habitats, ecosystems, biodiversity, etc. are not at all given. These are the reified form of past scientific theories and practices made in other laboratory situations at other times. My research in The Bahamas has been centered around contemporary laboratory situations which can be very generally referred to as social science, ecological and environmental research, and sustainable economic development- processes of human life and living, non-human life and living, and economies of visitation and investment. A focus on current events in The Bahamas could very well entail investigating any one of these arenas, and these realms are discursively separate in that they are often discussed as separate categories of inquiry which can be related post facto. But an investigation of The Bahamas as a living laboratory, as a site for active experimentation and exemplification, requires the recognition that these categories are interrelated and coconstitutional. Therefore, I should say at this point that I am working within my own laboratory situation with this dissertation in that I am, as mentioned above, conducting a sort of experiment by bringing a host of scholarly angles to bear on the situations and events I was and continue to be part of and witness to.For my purposes here, I will define a laboratory as a physical, conceptual, and designed space in which ideas can be tested and processes evaluated through experimentation. A laboratory implies scientific research. A laboratory space also implies that matter and materials are manipulated as part of the process of experimentation to achieve a desired outcome or to discover what comes out of a given design process. A living laboratory extends the notion of the physical and conceptual space for scientific research into “the field”- into “real” time and “real” life processes in situ, though this is importantly no less designed. Manipulation can then become the act of influencing pre-existing components and factors and even creating the possibility for the existence of those very factors. The living laboratory is thus a frame in which I call to attention the shifting relationship between fieldwork and the lab, which “traditionally” are separate physical and conceptual spaces- data in various forms is discovered, collected, and removed from the field, in which scientists are explorers and adventurers, and taken to the lab to be analyzed. A living lab merges the processes of exploration, discovery, collection, and analysis and alters what forms are acceptable and accessible as data. Field ecologists, biologists, and social scientists develop contingent relationships to fields based on specific forms of presence and practice. I have developed this observation in contrast to recent observations about the changing science of genomics in which the active presence of science in the field is said to have lessened and where scientists and students can “get in and out” with their data and samples without caring about the particular relationships and socialities of their field site.I argue that today, the field and the lab are synonymous and “the island is a laboratory” takes on a holistic and socialized meaning for the field life sciences- the what counts as experimental material or the subject of field research is increasingly designed as an amalgam of natural and social systemic processes. As I describe below, this has implications for defining what manner and matter of “life” the life sciences produce knowledge about.The panelists prescribed a form of research for a biocomplexity paradigm, stating that biocomplexity questions needed to be approached in an interdisciplinary manner and that they were different from typical research questions. The complex interactions that occur in the “real world” on multiple scales can only be understood through “combined efforts of scientists” from many disciplines who are allowed to work at the relevant “temporal and spatial scales.”

The modification of JA by jasmonate carboxyl methyltransferase converts it into the volatile compound methyl JA . This reaction is presumed to take place in the cytoplasm . MeJA mediates both developmental processes and defense responses against biotic and abiotic stresses . Additionaly, MeJA is a gaseous compound, and can thus act as airborne signals to mediate inter-plant communication. This means that neighboring plants can be signaled if stressed are present . Research has indicated that a positive feedback loop exists for JA biosynthesis . In Arabidopsis, VSP expression is selectively induced by JA and not OPDA, while both molecules induce defense responses. This demonstrates that multiple mechanisms are responsible for the transduction of JA-related signals, which are selectively activated in response to differing stimuli . The bacterial plant pathogen Pseudomonas syringae produces a JA-Ile-like compound termed coronatine , which suppresses some SA-immune responses by activating the JA signaling pathway . The Arabidopsis mutant coronatine-insensitive 1 was identified due to its insensitivity to plant growth inhibition by COR and OPDA . In addition, this mutant is male sterile and more susceptible to some pathogens and pests . COI1 encodes a 66-kD protein that contains an N-terminal F-box motif and a leucine-rich repeat domain . F-box proteins recruit regulatory proteins as substrates for ubiquitin-mediated degradation. This requires them to associate with Skp1 and Cullin to form an E3 ubiquitin ligase termed SCF complex which is important for JA responses .

JA–Ile facilitates binding of SCFCOI1 with the jasmonate ZIM-domain 1 protein . JAZ proteins are substrates for SCFCOI1 and negatively regulate JAresponses . In Arabidopsis these proteins belong to a 12 member family and contain a conserved motif at the C-terminus . Many JAZ mutants displayed no discernible phenotypes,vertical rack system possibly due to functional redundancy . Mutants of jaz10 are hypersensitive toJA, but the lack of obvious phenotypes in other jaz mutants suggests functional redundancy among other family members . The jaz1 mutant on ther other hand displayed male sterility, JA insensitivity, and increased resistance to infection by the bacterial pathogen P. syringae pv. tomato . The JAZ proteins homo- and hetero-dimerize by way of a conserved TIFY domain and also bind AtMYC2 and interact with COI1 through their C-terminal JAS domains . AtMYC2 is a helix-loop-helix transcription factor that acts as a key regulator of JA responses in plant-microbe interactions . When JA-Ile or COR bind to SCFCOI1 complexes, this promotes the ubiquitination of JAZ proteins leading to their degradation. Once degraded the JAZ-dependent repression on AtMYC2 is relieved and JA-responsive genes are activated . The JAZ proteins then recruit a co-repressor TOPLESS 8 and TPL related proteins through a adaptor protein called Novel Interactor of JAZ . NINJA and TPL proteins act as negative regulators of jasmonate responses . Resistance to specific pathogens conferred through JA signaling show little overlap in transcriptional changes. Molecular recognition of necrotrophic pathogens can trigger increased JA and ET synthesis as well as expression of defense genes, such as PDF1.2. Defensins, one group of ubiquitous peptides involved in innate immune response, are found in organisms ranging from invertebrates to plants. They are small , basic, cysteine-rich proteins encoded by multigene families, similar in complexity to those encoding other defense-related proteins . Defensins were first discovered in rabbits in 1984 and described in wheat and barley in 1990 .

PDF genes were later discovered in Arabidopsis and encode small peptides originally labeled as γ-thionins . γ-thionins were later renamed plant defensins to emphasize their structural similarity to mammalian defensins. The ancestry of defensins is thought to pre-date the divergence of plants and animals . Defensins are described in two separate kingdoms and further divided into five classes. Class 1, Class 2 and Class 3 are found in mammals and birds, while Classes 4 and are found in insects and Class 5 in plants . The primary structures of defensins vary between organisms. PDF proteins contain eight conserved cysteines . They also include a common fold, which is formed by a β-sheet and an α-helix steadied by disulfide bridges and capable of stabilizing the entire protein . Arabidopsis PDF genes can be separated into three families, each encoding closely related peptides. Family 1 consists of PDF1.1-1.5, family 2 consists of PDF2.1–2.6, and family 3 consists of At4g30070 and At5g38330 . The predicted mature peptide sequences encoded by PDF1.2a/b/c are identical. PDF1.2aand PDF1.2c form a tandem repeat on chromosome 5 and PDF1.2b is found on chromosome 2 directly adjacent to PDF1.3 . The high sequence similarity between PDF1.2a/b/c and PDF1.3indicates that little evolutionary time has passed since their duplication. More amino acid variability is evident within the second family but this family also has genes that occur in a tandem array . PDF2.1 is expressed specifically in roots, siliques, and seeds . PDF2.2 is expressed in all organs of healthy plants except stems and seeds . PDF2.3 is expressed in all organs excluding roots and is not upregulated in response to pathogen infection . PDF1.2a is induced in leaves upon infection of pathogens such as Botrytis cinerea . PDF1.1 expression is largely seed specific and may protect seedlings against pathogens . PDF1.1, 1.2, 2.1, 2.2 and 2.3 display distinct organ-specific expression patterns . PDF1.1, PDF2.1, PDF2.2 and PDF2.3 are expressed constitutively which means that most plant tissues constitutively express two or more defensin genes at any given time . Therefore, it is likely that specific peptides may be expressed during specific situations and sites . PDF1.4 and PDF2.4 appear not to contain predicted signal peptide sequences, suggesting they stay in the cytoplasm while the others PDF proteins are secreted.

Alternately, PDF proteins may overlap while acting distinctly to cover gaps in each-others’ activity spectrum . From the third family found within Arabidopsis, PDF3.2 encodes a protein of 129 amino acids with a C-terminal domain that has the conserved cysteine pattern shared by all plant defensins . PDF3.1 encodes 122 amino acids with 56% identical residues to the protein encoded by PDF3.2. These proteins could be fusion proteins or precursors but more research is necessary to determine their functions . Transgenic expression of PDF genes leads to fortification of tissues against pathogen attack. Two PDF proteins, one from dahlia and one from radish were found to inhibit the growth of Neurospora crassa. One observed response after infection with N. crassa is a change in fungal cell ion fluxes,mobile grow rack but this is believed to be a secondary effect, not a direct result of the PDF anti-fungal activity . There are two models describing possible modes-of action for the antimicrobial activity of PDF proteins. One model proposes that pores form in microbial cell membranes. The second model proposes that PDF proteins bind onto the anionic lipid head groups disrupting the stability of the phospholipid bilayer of microbial cell membranes . Binding sites for these PDF proteins to sphingolipids found on the cell surface in fungal membranes have been demonstrated . This suggests that the antimicrobial activity of PDF proteins is dependent on their ability to bind to a target in the membrane of an infecting pathogen . No similar activity has been shown against pathogenic fungi though. Aside from the many possible roles of PDF genes it has been established that many PDF proteins isolated to date display antifungal activities against a broad range of fungi. Monocot PDF proteins may also inhibit α-amylase, an enzyme found in insect guts . This possibly hampers the insect’s ability to digest plant material . It appears though while some alternately inhibit α-amylase activity and protein synthesis that PDF proteins do not display both activities concurrently. Additionally, most plant defensins do not display antibacterial activity which has been suggested to be a result of a infection pressure from fungal as opposed to bacterial pathogens on plants . Additional biological activities of PDF proteins include the ability to inhibit protein translation in a cell free system, inhibit proteases, and inhibit the growth of microbes . They may also act as mediators of zinc tolerance and inhibitors of ion channels, or exhibit activity against mammalian cells and enzymatic activity controlling the redox state of ascorbic acid . This diverse set of functions may be attributed to differences in the primary structures of defensins. PDF activities range from antimicrobial and insecticidal to anti-parasitic.

Due to their broad range of target organisms, PDF overexpression may be a suitable strategy for crop protection. While R-genes typically confer a narrow range of resistance, PDF genes may provide broad-spectrum resistance against multiple types of pathogens. If introduced into plants PDF genes may offer defensive advantages in addition to enhancing the plants ability to combat biotic stressors . Arabidopsis also contains over 300 Defensin-like genes and the evolution of DEFL-, PDF-, and R-genes bears remarkable similarity that may be due to their evolution through similar mechanisms . Members of these three groups can be found as single genes or in clusters, which arose through duplication, recombination, or diversifying selection . Cis-elements discovered within the promoter of PDF1.2b include a GCC box important for the ET response, a stress responsive G-box, a drought responsive element , and JA-responsive elements and . GCC boxes are commonly found in the promoters of genes which encode defenserelated proteins and are known binding sites for some AP2/ERF transcription factors . G-boxes regulate genes in response to environmental conditions such as red and UV light, anaerobiosis, and wounding and can be bound by certainbasic leucine zipper transcription factors . Transcription factors that positively affect PDF1.2b mRNA levels are the AP2/ERF-domain transcription factors ERF1, ORA59, AtERF1 and AtERF2, as well as the basic leucine zipper transcription factor TGA5 . Negative effects were observed upon over expression of AtERF4 or WRKY70, as well as in a triple mutant, where function of TGA2, TGA5 and TGA6, three redundantly acting TGA bZIP factors, is abolished . TGA2, TGA5 and TGA6 are also commonly required for the activation of JA- and ET-dependent defense mechanisms that counteract necrotrophic pathogens . TGA2 is the only transcription factor, for which direct interaction with the PDF1.2 promoter has been demonstrated yet . ORA59 and ERF1 are believed to bind directly to the promoter and AtERF1 and AtERF2 indirectly . ORA59 is the primary positive regulator of PDF1.2b expression in response to JA/ET and it binds GCC boxes . Since most PDF genes belong to small families of closely related members, studying their function can be difficult using traditional genetic methods. Hpa is a useful model pathogen to study the genetics of plant-pathogen interactions . However, unlike infections with bacterial pathogens, inoculation with Hpa does not result in synchronous and uniform responses in host plants. This is mainly due to the unsynchronized germination of Hpa spores upon spray inoculation. Furthermore, transcription factors and other regulators controlling defense responses are frequently represented by families of functionally redundant members . Additionally, some components of the plant immune system may be essential for plant survival during early development . Hence, conventional genetics is of limited use for the dissection of the plant defense network in this circumstance. Chemical genetics utilizes small molecules to alter in vivo protein functions in a reversible and highly controllable manner . Using such bioactive compounds as synthetic elicitors, a simultaneous and uniform activation of the defense network can be accomplished . This allows for reproducible measurements of the dynamics of molecular processes and physiological responses. In addition, synthetic elicitors may be used to simultaneously knock out families of functionally redundant proteins, theoretically resulting in clear phenotypes. Moreover, the function of essential genes can be studied efficiently by introducing the respective chemical at any stage of development to manipulate their activity . The identification of a collection of novel synthetic elicitors may permit the selective manipulation of defined branches of the defense network. Such elicitors will serve as powerful new tools for the emerging field of systems biology. They are likely to facilitate the stimulation of the defense network with unprecedented precision allowing the examination of the relation of defined signaling events and physiological outputs in a quantitative manner. In the broader context, the ability to manipulate disease resistance pathways using synthetic elicitors can also be exploited for agricultural purposes by using various combinations of chemicals to develop a new generation of pesticides.

Small molecules have the potential to simultaneously knockout the function of closely-related members of protein families . This may permit the study of biological functions of functionally redundant proteins. Using traditional genetics, this can be difficult or infeasible due to technical challenges and lethal phenotypes . Yet another advantage over traditional genetics is that bioactive small molecules allow for the study of essential gene functions at any stage in development because transiently active molecules can be added at any time point during plant development or applied at sub-lethal concentrations. In contrast, genetic mutations are permanent and the analysis of plant lines homozygous for a lethal mutation is challenging or impossible. Finally, multiple unrelated gene functions can be knocked out concurrently by using combinations of different bioactive molecules . For the primary screen,dutch buckets system both forward chemical and mutational screens must be specific, meaning that the read-out has to be specific and serve as an unambiguous proxy for the biological process of interest. Chemical genetics requires the screening of many thousands of chemicals in search of one with the ability to stimulate a particular response of interest . The need for chemicals that can manipulate a large diversity of biological processes resulted in the development of large structurally diverse chemical libraries . The concept of chemical genetics is based on the theoretical assumption that for every existing protein in the biosphere there are hypothetical organic structures capable of binding to it and interfering with its function .

The identification of bioactive compounds interfering with any given biological process or target protein requires screening of libraries representing a large diversity of chemical structures. Of key importance for the identification of bioactive compounds are their physicochemical properties. To be a biologically active compound the substance has to be “drug-like”, which means they must be capable of crossing biological membranes and to remain in an active state in the biological target tissue for a sufficient period of time . Lipinski’s ‘rule-of-five’ states that properties that favor bioactive compounds include a molecular weight of less than 500 g/mol, a lipophilicity value of more than five, less than five hydrogen-bond donors, and less than 10 hydrogen-bond acceptors . A large sample size of structurally distinct chemicals maximizes the probability that compounds will be identified that induce the desired biological effect. The identification of proteins targeted by a given compound is an integral step but also typically the bottleneck for most chemical genetics projects. Several strategies exist for target identification, some of those include: affinity chromatography, yeast three-hybrid , protein arrays, and screens for mutants with altered sensitivity to a compound of interest . In affinity chromatography, a compound is tagged and immobilized so that interacting proteins can be purified and then identified. In Y3H the compound of interest is tagged with dexamethasone or methotrexate and then applied to yeast cells. The compound then binds the DEX or MTX binding protein, which is fused to the DNA-binding domain of a transcription factor. The activation domain of the transcription factor is translationally fused to a cDNA library. When the compound interacts with a plant protein a complex is created and this results in the transcription of a reporter gene . In protein arrays a fluorescent- or isotope-labeled small molecule is used to screen protein chips . Finally, in a screen for mutants with altered sensitivity, mutagenized organisms are treated with compound and plants showing responses to the compound that differ from wild type are selected for further study .

There are several examples of successful applications of chemical genetics in plant systems. Armstrong et al., performed a high-throughput chemical screen using a 10,000 compound library with the intent of identifying inhibitors of auxin transcriptional activation . Their screening strategy involved the use of a line that expressed GUS in the root elongation zone after application of auxin. This screen resulted in the identification of 30 compounds showing strong inhibition of GUS expression. Four structurally distinct compounds were further studied based on low active concentrations . Two of these compounds impart phenotypes indicative of an altered auxin response, including impaired root development. The two strongest of these compounds displayed similar growth phenotypes after treatment. Additionally, microarray studies using the later two compounds indicated that similar transcriptional changes were induced by both inhibitors . Chemical genetics became popular in plant biology in the past 10 years and numerous successful applications of this approach in plants have been published during the past five years . In 2007 a number of successful chemical screens were reported. The compound 7-ethoxy-4-methyl chromen-2-one was discovered in a screen of 20,000-compound library based on its ability to cause a swollen root phenotype in Arabidopsis . Using live cell imaging of fluorescently labeled cellulose synthase and microtubules, DeBolt et al., showed that treatment with morlin interferes with cortical micro-tubules to alter the movement of cellulose synthase. This interference resulted in unique cytoskeletal defects which produced shorter and more bundled micro-tubules. Morlin proved highly useful for the study of mechanisms that regulate micro-tubule cortical array organization and how it interacts with cellulose synthase .

In a small screen of 120 bioactive molecules Arabidopsis seedlings were used to identify compounds that inhibited early immune responses. This screen resulted in four hits. These compounds reduced flg22 -activated gene expression of MAMP-responsive ATL2 gene. Two of these four compounds, triclosan and fluazinam, interfere with the accumulation of ROIs and transport of the FLS2 receptor. Additionally, the compound Triclosan, which blocks early immune responses, was used to determine a potential role for lipid signaling in flg22-triggered immunity . Hypostatin was discovered in screens as a compound that inhibits hypocotyl growth in a Arabidopsis accession dependent manner . 11 other accession-selective hit molecules were also identified alongside hypostatin, which is an inhibitor of cell expansion. Additionally, a screen for compounds able to disturb microfibril-cellulose attachment resulted in the identification of cobtorin . This study demonstrated that different Arabidopsis accessions can be used to study the activity of interesting new compounds. The enhancement of plant immune responses by exogenous application of chemicals can be traced back to the treatment of tobacco with SA . While SA, JA, and ET can induce defense response, their use in the field or greenhouse setting is restricted based on their shortcomings as defense inducers that are broadly effective on many plant species . The use of environmentally safe plant defense-inducing chemicals, which boost a plant’s innate immune responses, offers an attractive alternative to pesticides. Linda wants me to reference the body of literature that explored SAR inducers as methods of control – klessig + sa An alternative procedure to protect plants against disease is to activate their own defense mechanisms by specific biotic or abiotic elicitors . The classical type of induced resistance is often referred to as systemic acquired resistance . Sodium salicylate , 2,6- dichloroisonicotinic acid , and benzothiadiazole-S-methyl ester are well-known elicitors of SAR in various plants against disease . The expression of SAR, triggered by either pathogen infection or treatment with NaSA or its functional analogs INA or BTH, is tightly associated with the transcriptional activation of genes encoding pathogenesisrelated proteins . The nonprotein amino acid DL-3-aminon-butanoic acid also activates an induced resistance response. BABA induced resistance, involves SA-dependent, SA independent,dutch buckets and ABA-dependent defense mechanisms, and the importance of these defenses varies according to the nature of the challenging pathogen . Many molecules exist that cause an induction of defenses in plants when applied.

Plant-derived small molecules other than SA, JA, and ET have been identified as important to controlling or preventing disease in plants. Some of these phytohormones include abscisic acid , brassinosteroids, gibberellin, cytokinin, and auxin . Like the interactions between SA, JA and ET, other molecules are important for the tailoring of defense responses . Activation of ABA signaling processes and its biosynthesis have also been shown to promote plant disease . Alternatively, brassinosteroid treatment has been shown to enhance resistance against some biotrophs, mediate abiotic stress responses through NPR1, and induce PR1 expression . Gibberellic acid can induce increases in ROS accumulation and attenuation of JA signaling . Cytokinins, which affect cell division and morphogenesis, can also enhance the SA response and thus promote resistance against biotrophs . Finally, auxin signaling may suppress SA biosynthesis and signaling, while SA attenuates auxin signaling . These plant hormones are integral to the function of plants. While many of these hormones were not originally associated with defense, new research suggests they all have roles in coordinating plant response to pathogen invasion. Every year billions of dollars are spent on pesticides which leave residues on produce that control pests and pathogens but can be harmful to consumers and the environment. Such off-target effects make the study of interactions between plants and pathogens an integral field for the reduction of conventional pesticide use. Using model pathosystems, such as Arabidopsis thalianaand Hyaloperonospora arabidopsidis , many important questions related to plant disease resistance are being addressed. A complex transcriptional network controls plant immune responses. Of key importance for the regulation of this defense network, are protein kinases that act at various stages during defense activation. Chemical genomics can be used to study these different stages. Plant defense-inducing molecules identified and characterized using chemical genomics will be valuable tools for the dissection of the plant defense network and will serve as leads for the development of novel environmentally safe pesticides. Genes from the Arabidopsis ACIDcluster are coordinately inducible by the synthetic elicitors DCA and INA. This cluster is enriched for genes encoding protein kinases. Using a forward genetics approach it was demonstrated that 10 of 16 ACID members tested are required for full immunity of Arabidopsis against Hpa. Seven of these 10 ACID members have not been implicated in plant immunity before. In addition, eight novel synthetic elicitors identified and characterized via chemical genomics were reported on here, one of which, called CMP442, is a more potent defense inducer than DCA or INA. While effective in crop protection pesticides leave residues on produce and have off target effects . This makes the design of novel green pesticides highly attractive. Also, the elucidation of the finer points of interactions between plant and pathogen is integral for the design of new approaches to more efficiently and safely prevent crop diseases. The model plant Arabidopsis thaliana and the oomycete Hyaloperonospora arabidopsidis are a naturally coevolving pathosystem with a high level of intra-species genetic diversity . Use of this and other model interactions has revealed that plants have a complex inducible immune system that protects wild species and crops from pathogen infections. When plants recognize the presence of an infecting pathogen, a multitude of signaling events are triggered that ultimately lead to efficient defense . Some of the early responses after resistance -gene recognition include changes in ion fluxes, synthesis of reactive oxygen species , alterations in gene transcription, which can be followed by a hypersensitive response , where the plant cells surrounding the point of infection die to restrict pathogen growth . An ancient and fundamental form of plant defense involves conserved microbe-associated molecular patterns . MAMPs are recognized by plant pattern-recognition receptors resulting in the activation of a complex defense response. This form of plant immunity is referred to as pattern-triggered immunity . A second form of immunity is based upon the recognition of pathogen-secreted effector molecules, which are proteins that promote pathogen virulence in the plant. Here the plant is capable of recognizing the presence of pathogen effectors, or their cellular effects, by disease Rproteins. R-proteins constitute a second class of plant immune receptors, besides PRRs, and induce a strong defense response, which often includes HR. This form of immunity is called effector-triggered immunity . In the absence of a cognate R-protein, the secretion of effectors enables pathogens to successfully infect their hosts. During such compatible interactions, plants can still mount a weakened immune response, called basal defense. Basal defense typically limits the spread of pathogens but is not capable of fully preventing disease .

Trifoliate orange, known for its high-quality fruit and tolerance to various biotic and abiotic stressors was compared to rough lemon which historically produces high yield and large fruit that are lacking in flavor. In Chapter 1, I report a detailed analysis of the temporal changes and genotypic differences in gene and miRNA expression in root tissue of different root stocks. To the best of my knowledge, this is the first comparison of root transcriptomes performed in citrus. In Chapter 2, expression data from fruit of trees grafted onto the four different root stocks was assessed. Changes in expression throughout development were linked to fruit quality variation. Additionally, the role of miRNAs in regulating the biological and metabolic processes that were affected in each of these chapters was investigated. The results provide a global examination of the molecular mechanisms underlying graft-induced changes in citrus fruit development and ripening. Citrus is grown in more than 140 countries and is one of the most economically important crops in the world. The total production of citrus in the United States in the 2018 growing season was 6.1 million tons on a total of 679 thousand acres. California produced 58 percent of the United States total, producing 3.6 million tons of citrus on 278 thousand acres. Approximately 75 percent of California’s citrus production is sold to the fresh market opposed to being processed into other commodities, such as juice. Oranges accounted for 64 percent of the total citrus produced in the United States and were valued at $1.8 billion, according to the United States Department of Agriculture. Citrus trees are rarely grown from seed and virtually all commercial citrus is propagated by grafting.

This reduces the juvenile phase,hydroponic gutter allowing for the trees to produce fruit many years earlier than those grown from seed. Root stocks impart certain traits onto the scion and the effects of root stocks can be large. The most significant impacts are on growth and vigor, tree nutrition, stress resistance, and fruit quality. In citrus, phenotypic differences in fruit quality have been well documented. However, understanding of the molecular mechanisms underlying these differences is lacking, especially regulatory mechanisms. Previous studies in apple, grape, sweet cherry, and other fruit crops have examined transcriptome changes in various root stock-scion combinations. In citrus, gene expression profiling has been used to understand root stock effects on growth of trees and responses to biotic and abiotic factors. Many transcriptomic studies have also been performed in citrus to elucidate fruit ripening and development in commonly grown citrus cultivars. To date, none of these reports have linked the genetic effects of citrus root stocks to fruit quality. Fruit growth and development and the mechanisms underlying fruit quality are complex. Signal transduction systems regulate many aspects of fruit ripening32. During citrus development, the ABA-signal pathway may act as a central regulator of ripening, combined with other hormones, including auxin and ethylene. A recent study showed that ABA is a positive regulator of citrus ripening and exogenously applied ABA regulates citrus fruit maturation, suggesting that ABA metabolism plays a crucial role in citrus fruit development and ripening35. Previous studies identified Protein phosphatase 2C family proteins as negative regulators of ABA signaling. PP2C dephosphorylates and inactivates a SNF1-related kinases family 2 protein, which is a positive regulator of ABA-response pathways.

Plants with an inactive form of PP2C were hypersensitive to ABA, causing increased activation of ABA-responsive genes. ABA-signaling response has also been linked with drought-stress tolerance. This study suggested that ABA accumulation is associated with a decrease in relative water content and Romero et al. suggest that ABA increases caused by dehydration upregulate levels of PP2C. Auxin, another phytohormone important for fleshy fruit development, regulates many growth and development processes. The auxin-signaling pathway regulates transcription of hundreds of auxin-inducible genes. Promoters of these auxin-responsive genes contain auxin-responsive elements , which bind the auxin-response factor family of transcription factors. ARF activity is regulated in part by Aux/IAA genes, which are transcriptional repressors of the auxin response. In the absence of auxin, Aux/IAA proteins dimerize with ARFs and recruit corepressors of the TOPLESS family, which in turn recruit chromatin-remodeling proteins that stabilize the repressed state. When auxin is present, it acts as a “glue” between Aux/IAAs and F-box proteins that are part of a ubiquitin protein ligase complex. This causes polyubiquitination and subsequent degradation of Aux/IAAs, which releases its repression, leading to the activation of auxin-regulated genes. Together with ABA and other hormones, auxin regulates several aspects of fruit development, including fruit set, fruit size, and ripening related events. Additionally, prior studies have indicated that small RNAs may play a regulatory role in fruit development and ripening. Small RNAs are a type of single-stranded, non-coding RNA that is typically 20-24 nucleotides in length, of which microRNAs are the most extensively researched class and are known to post-transcriptionally down regulate the expression of target mRNAs through mRNA cleavage or translational inhibition.

In strawberry, miR159 was shown to act as a ripening regulator by targeting a MYB transcription factor, which plays a crucial role in the ripening process51. Several examples of miRNA involvement in fruit development and maturation have been described in a variety of crop species, including apple, grape, peach, blueberry, date palm, and tomato. miRNAs that suppress specific transcription factors that are thought to be regulators of citrus fruit development and ripening have also been identified58. However, the expression profiles of miRNAs in various scion-root stock combinations and their subsequent impact on fruit quality have not yet been evaluated. In this study, trees grafted on four root stocks were chosen from a root stock trial at the University of California, Riverside to assess for various fruit quality traits; Argentina sweet orange, Schaub rough lemon, Carrizo citrange, and Rich 16-6 trifoliate orange. In general, rough lemon root stocks produce the highest yield and fruit size, but fruit is of lower quality, containing lower acidity and lower levels of total soluble solids, also known as the “dilution effect”. On the other hand, trees on trifoliate orange produce smaller, high quality fruit with high yield on often smaller trees. Carrizo citrange root stocks produce intermediate yield with good fruit quality. Sweet orange root stocks produce good quality fruit, but trees are very susceptible to various citrus diseases. An RNA-seq approach was implemented to investigate differences in gene expression in fruit due to genetically varying root stocks,hydroponic nft channel with the aim of identifying genes that could potentially play a role in improvement of fruit quality.

Furthermore, miRNA expression profiles were obtained for each of the root stocks to identify potential regulatory mechanisms associated with their target genes.Fruit were harvested in January at the end of the 2016 growing season when fruit were ripe. Total yield was recorded. Ten fresh fruit per tree were collected and analyzed for the following traits: weight, height, width, rind color, rind texture, peel thickness, internal texture and taste. The juice was then pooled from all ten fruit and percent juice, total titratable acid , and total soluble solids for each pool were calculated at the UC ANR Lind cove Research and Extension Center. The average for each trait of the ten fruit per tree were considered one biological replicate and ten biological replicate trees were sampled for statistical analyses. Statistical differences in fruit quality between fruit from trees on different root stocks were evaluated using an analysis of variance test and Chi-squared test. The differences among treatment means were evaluated by Fisher’s Least Significant Difference test and Duncan’s Multiple Range Test. Data were considered to be statistically significant when P < 0.05.The juice vesicles of three representative fruit per tree from two biological replicates of each of the four root stock genotypes at the four collection time points were subjected to RNA-seq . Samples were ground in liquid nitrogen and total RNA was extracted from ~200 mg tissue using the ZR Plant RNA MiniPrep™ kit per manufacturer’s instructions. An Agilent Bioanalyzer was used to confirm the integrity of the total RNA. The RNA with a RIN value greater than seven qualified for RNA-seq. For messenger RNA-seq, sequencing libraries were created using TruSeq Stranded mRNA Library Preparation Kit according to the manufacturer’s protocol. For small RNA-seq, sequencing libraries were created using TruSeq Small RNA Library Preparation Kit according to the manufacturer’s protocol. Each library was prepared for multiplexing with a unique indexed primer. Quantification of all libraries was performed with Nanodrop and Qubit fluorometer. The library size distribution and quality were measured with an Agilent Bioanalyzer. Multiplexed libraries were sequenced in a single lane on an Illumina NextSeq 500 instrument at the University of California, Riverside Genomics Core facility. An average of 11 samples were sequenced per lane. The data analysis was carried out using the RNA-seq workflow module of the systemPipeR package available on Bioconductor60.

Quality reports were created with the FastQC function. Citrus clementina v 1.0 genome assembly and annotations were downloaded from JGI’s portal . Sequencing reads were then mapped against the Citrus clementina v 1.0 reference genome using the Bowtie2 alignment suite for small RNAs and HISAT2 alignment suite for messenger RNAs. Messenger RNA raw reads were counted in a strand-specific manner. Known miRNA gene coordinates, required for counting, were acquired by downloading all known plant miRNAs from the plant miRNA database, aligning these sequences to the Citrus clementina v 1.0 reference genome using Bowtie2 with perfect alignment, and extracting the alignment coordinates. Small RNA raw reads were then counted at the known miRNA locations using the summarize Overlaps function. Sample-wise correlation analysis was performed using rlog transformed expression values generated by the DESeq2 package. In this study, RNA-seq generated reads that mapped to 19,359, 19,124, 19,336, and 19,374 citrus genes in samples from fruit of trees grafted onto sweet orange, Carrizo citrange, rough lemon, and trifoliate orange root stocks, respectively. With criterium of at least 2-fold difference and a p-value less than 0.05 , a total of 1,633 differentially expressed genes were identified between genotypes at one or more time points . There were 684 genes found to be DE between rough lemon and sweet orange root stocks, 388 DEGs between Carrizo citrange and sweet orange, 361 DEGs between trifoliate orange and sweet orange, 178 DEGs between rough lemon and Carrizo citrange, 395 DEGs between trifoliate orange and Carrizo citrange, and 855 DEGs between trifoliate and rough lemon. None of these DEGs overlapped in all 6 comparisons . The majority of the DEGs were specific to one pairwise comparison, but the largest overlap of was a group of 122 DEGs that were commonly shared between RL-SO, CZ-SO, TF-RL, and TF-CZ. Due to the large number of DEGs observed between fruit grafted onto trifoliate orange and rough lemon root stocks and the fact that the largest phenotypic differences in fruit quality traits were generally seen when comparing fruit grown on these root stocks, we primarily focused on this contrast for the remainder of this study. DEGs uniquely belonging to this comparison are more likely to play a role in the phenotypic changes seen when fruit are grown on trifoliate orange versus rough lemon root stock. Gene Ontology and pathway enrichment analyses were conducted to explore the functions of genes that were DE in trees on different root stocks. GO categorization showed that the molecular function GO terms ‘DNA-binding transcription factor activity’ and ‘transferase activity’ were significantly enriched . Genes associated with photosynthesis and located in the photosynthetic membrane were also enriched . KEGG pathway analysis revealed that genes for plant-hormone signal transduction, carotenoid biosynthesis, and fructose and mannose metabolism were significantly enriched when comparing fruit grown on trifoliate to rough lemon root stocks . The hormone-signaling-related pathway included DEGs involved in auxin, gibberellin , abscisic acid , ethylene , and jasmonic acid signaling . Visualization of fold changes using MapMan software revealed that several genes in the ABA and GA pathways were down-regulated in fruit grown on rough lemon compared to trifoliate root stocks.Many genes involved in other cellular responses, as well as transporters were also DE . To further understand the genetic influence of root stocks on fruit quality, we focused on the expression changes of miRNAs and their target genes.