Author: ecogrow

More generally, on the time scale of centuries, marine transgression may cause rapid salinization of entire aquifers.In Western Europe Holocene transgressions of a few thousands of years have brought salt water of corresponding age to a depth of over 200 m.Nevertheless, at many places all around the world fresh and brackish waters have been found on the continental shelves.Numerical modeling by Post and Simmons illustrates how low-permeability lenses protect fresh water from mixing with downward invading overlying saline ocean waters with higher density.Van Duijn et al.gave a general, modern stability analysis of such density stratified flows below a ponded surface.Saltwater intrusion by tides in the mouths of rivers—The Zuiderzee Works and Delta Plan stopped salinization from tidal motion in the North.In the Southwestern Delta, tidal motion was only partly eliminated and no major freshwater reservoirs are available, like the Lakes IJssel and Marken for the northern provinces.Instead, fresh water supply in the southwest comes more directly from diversions of water from the major rivers.In the 20th century the quality of the Rhine water gradually deteriorated, until a series of international treaties brought improvement.The river water quality was further reduced by an inward directed flow of high-density saline water underneath the outward directed flow of lighter runoff water.Traditionally, the tides had free play and salinized the river water far inland,vertical farm particularly in periods of low river flows.As a result of this salinization, in the 1970s the surface water in the important West land greenhouse district between Rotterdam and the Hague was hardly suitable for use as irrigation water.

The growers themselves made it even worse using drainage return flows, resulting from high leaching fractions combined with high application of fertilizers.The RAND corporation did a policy analysis of water management for the Netherlands , balancing engineering ambitions and agricultural interests, specifically regarding the desired irrigation water quality for use in greenhouse horticulture.The Delta Works have provided some relief from saltwater intrusion in river mouths; however, conflicting agricultural and environmental interests continue to dominate the discussion about seawater blockage as related to the desire to maintain brackish aquatic ecosystems.Saltwater intrusion by inward flow of water to land below sea-level—Fig.32 shows the depth of the brackish-fresh interface in the coastal regions of the Netherlands.Similar maps are available for the coastal region of Belgium.Because fresh water is floating on top of saline groundwater in the dunes area along the west coast, saline intrusion is strongest in the North and Southwest, where coastal dunes are absent.At numerous locations in the dunes, fresh dune water is pumped as a source for preparing drinking water for the western part of the country, where the groundwater is too saline because of continued saltwater intrusion.For example, a dune area of 3400 ha along the western coast supplies fresh drinking water to Amsterdam, already since 1853.To keep the floating bodies of fresh water in the dunes intact, the freshwater pumping is compensated for by excess rainfall and infiltration of river water, partly after having been stored in the Lakes IJssel and Marken.Fresh water floating on top of salt water in agricultural fields—Recently fresh water lenses floating on top of saline groundwater have been fully recognized as being of great importance, not only in the dunes, but also in farmer fields along coastal regions where upward seepage of saline groundwater occurs.

These freshwater lenses can come from rain, melted snow, and increasingly also from irrigation of agricultural lands.Eeman et al.made a detailed analysis of the thickness of a freshwater lens and the transition zone between this lens and the up welling saline water.Starting from a fully saline condition between drains or ditches and assuming constant rates of saltwater up welling and freshwater infiltration, they showed that a freshwater lens will grow until it reaches a maximum size.Moreover, they concluded that the fresh/saline ratio of the drainage water will change from zero to the infiltration/upward seepage ratio.However, as shown by others , seasonal variations of infiltration and plant root withdrawal of fresh water will cause temporal fluctuations of the thickness of the lenses and the fresh-saline ratio of the drainage water.Salt tolerance in a generally humid and cool climate—Most salt tolerance data for field crops and flower species date from before 2000 and were reviewed by Van Bakel et al.and Stuyt et al..The latter compilation in Dutch is the most complete, providing salt tolerance thresholds for35 individual crops or groups of crops.Salt tolerance data for greenhouse horticultural crops were brought together by Sonneveld and Sonneveld and Voogt,and included interactions between plant nutrition and salinity.In the last decade, salt tolerance tests have been carried out at Salt Farm Texel.The 160 m2 experimental plots were irrigated, using eight replications of seven different salt concentrations, obtained by mixing saline seawater with fresh water.Because of the high hydraulic conductivity of the soil, it was possible to maintain the desired concentration throughout the root zone, irrespective of the weather in the growing season.Salt tolerance was tested for six crops: potato , carrot , onion , lettuce , cabbage , and barley.The data were analyzed using the Maas and Hoffman and Van Genuchten and Gupta models.

An alternative model based on the Dalton-Fiscus model for simultaneous uptake of water and solutes was explored by Van Ieperen.Salinization in the countries around the North Sea—In principle, the lowland coastal regions of Belgium, Germany, the Netherlands, Sweden, and the United Kingdom face similar threats from salinity as in the Netherlands.For example, there was widespread flooding of farmland along the UK east coast during the Southern North Sea storm of December 5, 2013.Due to different economic and political priorities, the responses to such events have varied.The Netherlands was saved potential disastrous flooding in 2013, thanks to the Delta Plan response to the 1953 Storm Flood.Gould et al.analyzed the impact of coastal flooding on agriculture in Lincolnshire, UK.They noted that flood risk assessments typically emphasize the economic consequences of coastal flooding on urban areas and national infrastructure and tend to omit the long-term impact of salinization of agricultural land.Considering this long-term salinization, they calculated financial losses ranging from £1366/ha to £5526/ha per inundation, which would be reduced by between 35% up to 85% by post-flood switching to more salt-tolerant crops.Egyptians have practiced irrigated agriculture for about 5000 years in the Nile River valley, using basin irrigation dependent on the rise and fall of flows in the Nile river.Since 3000BCE, the Egyptians used to construct earthen banks to form flood basins of various sizes, filled with the Nile water to saturate soils for crop production.Egyptian irrigated agriculture has been sustainable for thousands of years,nft vertical farming in contrast to other civilizations in Mesopotamia.Reasons were provided by Hillel , pointing to the annual natural flooding that deposited nutrient-rich soil material,annual cycles of rising and falling of the Nile river that created fluctuations of the groundwater table and yearly flushing of salts of its narrow irrigated flood plains, and the annual inundations that occurred in the late summer and early fall, after the spring growing season.With the construction of the Aswan High Dam, most of the land was converted to perennial irrigation and the irrigated area increased from 2.8 to 4.1Mha.The year-around irrigation and lack of leaching by annual pulsing of the Nile river triggered soil salinization.More than 80% of Egypt’s Nile water share is used in agriculture.Water- saving in agriculture is a major challenge because annual per capita water availability in Egypt is expected to decrease to 560m3 from a current level of 950m3.The salts of the Nile basin are either of intrinsic origin, sea water intrusion or from irrigation with saline groundwater.Since the climate of Egypt is characterized as arid with annual rainfall ranging from 5 to 200mm compared to evaporation rates of 1500–2400mm, crop production is not possible in most parts of Egypt without irrigation.Salinity problems in the irrigated areas are widespread and about 1 million ha are already affected.At present only 5.4% of the land resources in Egypt is of excellent quality, while about 42% is relatively poor due to salinity and sodicity problems.Soils in the Nile valley and the Delta are Vertisols, characterized by substantial expansion by wetting and shrinking by drying.In Egypt, productive lands are finite and irreplaceable and thus should be carefully managed and protected against all forms of degradation.Other countries of the Nile basin also have salinity problems.Kenya has about 5Mha of salt-affected lands.In Tanzania, about 30% area is characterized by poor drainage and soil salinity problems.The soil salinity problems in countries such as DR Congo, Uganda, Burundi, and Rwanda are less prevalent however soils are low in fertility.The salt-affected lands in South Sudan and Sudan are in the White Nile irrigation schemes.This area has hardly been utilized for agricultural production despite having great potential due to the availability of water from Nile.In other parts of South Sudan, low soil fertility and lack of good quality seeds for crops and forages are the major bottlenecks in the development of agriculture.

Ethiopia stands first in Africa in the extent of salt-affected soils with an estimated 11Mha of land exposed to salinity.This corresponds to 9% of the total land area and 13% of the irrigated area of the country.These soils are concentrated in the Rift Valley, Wabi Shebelle River Basin, the Denakil Plains and other lowlands and valleys of the country, where 9% of the population lives.Currently, soil salinity is recognized as the most critical problem in the lowlands of the country resulting in reduced crop yields, low farm incomes and increased poverty.The insufficient drainage facilities, poor-quality groundwater for irrigation and inadequate on-farm water management practices are usually held responsible for the increasing salinity problems.Despite the widespread occurrence of salt-affected soils, Ethiopia does not have an accurate data base on the extent, distribution, and causes of salinity development.Most of the saline soils are concentrated in the plain lands of the Rift Valley System, Somali lowlands in the Wabi Shebelle River Basin, the Denakil Plains and various other lowlands and valley bottoms throughout the country.The introduction of large-scale irrigation schemes without the installation of appropriate drainage systems have also resulted in the rapid expansion of soil salinity and sodicity problems in the lower Wabi Shebelle basin of Gode.The distribution of surface salinity in the four largest regions of Ethiopia is given in Table 5.Sudan has built four dams on the Nile during the last century to provide irrigation water to an additional 18,000 km2 of land.This has made Sudan the second most extensive user of the Nile river water, after Egypt.Despite these arrangements, Sudan has not achieved full production potential due to lack of water infrastructure for equitable water distribution among farmers, lack of farm inputs and low soil fertility conditions.In Egypt, about 85% of the available water resources are consumed by the agriculture sector.The completion of Aswan dam increased the intensity of irrigation, which created water logging problems in many parts contributing to the pollution of land and water resources.In Egypt, surface and subsurface drainage systems have been installed to control rising water tables and soil salinity.Besides, crop-based management is used to combat soil salinization.Farmers were encouraged to use agricultural drainage water to irrigate crops thereby reducing disposal problems.However, the unregulated application of drainage water for irrigation has reduced crop yields and polluted soil and water resources.In addition to agricultural chemical residues and salts, drainage waters include treated and untreated domestic wastewater.The use of organic amendments and the mixed application of farmyard manure and gypsum was useful in reducing soil salinity and sodicity.Recently, phytoremediation or plant-based reclamation has been introduced in Sudan, for example to reduce soil sodicity instead of using gypsum.In the absence of surface and subsurface drainage systems, farmers in Ethiopia continue to manage salt-affected soils by adopting traditional salt management solutions.These include:direct leaching of salts,planting salt-tolerant crops,domestication of native wild halophytes for agropastoral systems,phytoremediation,chemical amelioration, and the use of organic amendments such as animal compost.Farmers have also used various drainage designs, allowing salts to settle before its reuse for irrigation water.However, all such practices have failed to mitigate salinity problems in the long-term.Hence crop yields continue to decline, resulting in reduced farm incomes, food shortage and increased poverty.Many of the smallholder farmers are also working as daily laborers, causing unprecedented farmer migration to nearby urban areas and exacerbating prevalent problems of urban unemployment.The increasing demand for food for the rising population in Egypt , the country is trying to expand its irrigated agricultural area.

As pointed out in this review of the role of microorganism to mitigate abiotic plant stresses, their use can open new and emerging applications in agriculture and also provide excellent models for understanding stress tolerance, potentially to be engineered into crop plants to cope with abiotic stresses such as soil salinity.In another study by Marks et al.it was demonstrated that dramatic changes in salinity of salt marsh soils as caused by storm surges or freshwater diversions can greatly affect denitrification rates, which is especially relevant for nutrient removal management of eutrophic waters such as for the Mississippi delta.Rath et al.studied such dynamic conditions by the bacterial response to drying-rewetting in saline soils and concluded that increased soil salinity prolonged the time required by soil microbes to recover from drought, both in terms of their growth and respiration.Biochar is defined as organic matter that is carbonized by heating in an oxygen-limited environment.The properties of biochar vary widely, dependent on the feed stock and the conditions of production.Biochar is relatively resistant to decomposition compared with fresh organic matter or compost, and thus represents a long-term carbon store.Biochar stability is estimated to range from decades to thousands of years,ebb flow but its stability decreases as ambient temperature increases.It has been shown that application of biochar to soil can improve soil chemical, physical and biological attributes, enhancing productivity and resilience to climate change, while also delivering climate-change mitigation through carbon sequestration and reduction in GHG emissions.

Chaganti et al.evaluated the potential of using biochar to remediate saline–sodic soils in combination with various other organic amendments using reclaimed water with moderate SAR.Results showed that leaching with moderate SAR water was effective in reducing the soil salinity and sodicity of all investigated soils, irrespective of amendment application.However, it was shown that combined applications of gypsum with organic amendments were more effective to remediate saline–sodic soils, and therefore could have a supplementary benefit of accelerating the reclamation process.Akhtar et al.used a greenhouse experiment to show that biochar amendment for a different soil salinity levels could alleviate the negative impacts of salt stress in a wheat crop through reduced plant sodium uptake due to its high adsorption capacity, decreasing osmotic stress by enhancing soil moisture content, and by releasing mineral nutrients into the soil solution.However, it was recommended that more detailed field studies must be conducted to evaluate the long-term residual effects of biochar.The application of marginal waters to augment irrigation water supplies particularly has led to investigations to evaluate plant nutrient uptake impact of saline-sodic soils.It has been shown that soil salinity can induce elemental nutrient deficiencies or imbalances in plants depending on ionic composition of the soil solution, due their effect on nutrient availability, competitive uptake, transport, and partitioning within the plant.Most obviously, soil salinity affects nutrient ion activities and produces extreme ion ratios in soil solution.

As a result, for example, excess Na+ can cause sodium-induced Ca2+ or K+ deficiency in many crops.Nutrient uptake and accumulation by plants is often reduced under saline soil conditions because of competition between the nutrient in question and other major salt species, such as by sodium-induced potassium deficiency in sodic soils.Soil salinity is expected to interact with nitrogen both as competition between NO 3 and Cl ions in uptake processes as high chloride concentrations may reduce nitrate uptake and plant development , and indirectly through disruptions of symbiotic N2 fixation systems.Interactions with phosphorus vary with plant genotype and external salinity and P concentrations in soil solution, which are highly dependent on soil surface properties.Calcium magnesium and sulfur as well as micro-nutrients all interact with soil salinity, Na and one another.Imbalance of these elements cause various pathologies in plants including susceptibility to biotic stresses.Among potential alternative land uses of saline soils is their economic potential for biomass production using forestry plantations , as many tree species are less susceptible to soil salinity and sodicity than agricultural crops.A thorough review of the economic potential of bioenergy from salt-affected soils has been presented by Wicke et al..Using the FAO soil salinity database, they estimated that the global economic potential of biosaline forestry is about 53 EJy 1 , when including agricultural land, and to 39 EJ y 1 when excluding agricultural land.

Plantation forestry has been advocated to control dryland salinity conditions, with fast growing versatile Eucalyptus species to lower shallow groundwater tables, however, salinity/sodic stresses in the long-term prohibit significant economic returns.Much will depend on regional production costs.Studies have shown that biosaline forestry may contribute significantly to energy supply in certain regions, such as sub-Saharan Africaand South Asia, and has additional benefits of improving soil quality and soil carbon sequestration , thus justifying investigating biosaline forestry in the near future.Economic losses of productive land by salinization are difficult to assess, however, various evaluations have reported annual costs of US $250–500/ha , suggesting a total annual economic loss of US$30 billion globally.As pointed out by Qadir et al., a large fraction of salt-affected land is farmed by smallholder farmers in Asia and SSA, necessitating off-farm supplemental income activities, with others leaving their land for work in cities.Given that much of the projected global population growth is in those regions, prioritization of research and infrastructure investments to mitigate agricultural production impacts there is extremely relevant.A thorough analysis of the production losses and costs of salt-induced land degradation was done by Qadir et al., based on crop yield losses, however, they point to the need to also consider additional losses such as by unemployment, health effects, infrastructure deterioration, and environmental costs.Their calculations compared economic benefits using cost-benefit analysis of “no action” vs “action” for various case studies.A yield gap analysis by Orton et al.for wheat production in Australia showed that soil sodicity alone represented 8% of the total wheat yield gap, representing more than AUS $1 billion.In their sustainability assessment of the expanding irrigation in the western US, comparing real outcomes with those predicted by Reisnerin this book Cadillac Desert, Sabo et al.included an economic analysis of agricultural revenue losses as a result of the increased soil salinity for the western US.Using the USDA NRCS soil’s data base, and available crop salt tolerance information,greenhouse benches they estimated a total annual revenue loss by reduced crop yields of 2.8 billion US dollars.In all, land values of salinized lands depreciate significantly and incur huge economic impact, putting into question the sustainability of agricultural land practices that induce soil salinization.Australia is the world’s driest inhabited continent with an average annual rainfall of 420 mm with a high potential for the formation of salt-affected landscapes.Development of agricultural practices in Australia began after the European settlement and was widely adopted during 20th century.Earlier, the indigenous population found their food by hunting and foraging.They indirectly depended on soils for plant food, but they did so without soil management.The European settlers were unaware of the soil characteristics they had to work with.Salt has been accumulating in the Australian landscape over thousands of years through small quantities blown in from the ocean by wind and rain.In addition to mineral weathering, salt accumulation is also associated with parna, a wind-blown dust coming from the west and the south-west of the continent.

Many soils of the arid to sub-humid regions of Australia contain significant amounts of water-soluble salts, dominantly as sodium chloride.Their dense sub-soils are frequently characterized by moderate to high amounts of exchangeable sodium and magnesium , and are generally named duplex soils.Discussing the genesis and distributions of saline and sodic soils in Australia, Isbell et al.concluded that salts from a variety of sources have probably contributed to the present saline and sodic soils.In the early part of 20th century, the Australian government initiated a nation-wide soil survey with soil analysis.As early as the 1930s, soil surveys in the Salmon Gums district, Western Australia, found that salt accumulation in surface and subsoils occurred in more than 50% of the 0.25 million ha surveyed.These surveys also found that virgin areas had higher accumulations of salts in the upper meter than in vegetation-cleared areas for the major soil types.In one of his earlier observations in the Mallee region of Southern Australia, Holmes found a salt bulge that was more than 4 m below the surface in a virgin heath community.Northcote and Skene , examining numerous data relating to the morphology, salinity, alkalinity, and sodicity of Australian soils presented the areal distribution of saline and sodic soils in Australia, using the classification of salt-affected soils of Table 2.While 32.9% of the total area in Australia is salt-affected, sodic soils occupy 27.6% of this area.Hence, most of the research during the middle of the 20th century focused on sodic soils and their management.Northcote and Skene defined sodic soils as those having an ESP between 6 and 14, and strongly sodic soils as those having an ESP of 15 or more.The recent Australian soil classification defined “Sodosols”as soils with an ESP greater than 6.However, soils with ESP 25–30 were excluded from sodosols, because of their very different land-use properties.California’s natural geology, hydrology and geography create different forms of salinity problems across the state, ranging from sea water intrusion induced salinity along the central coast to concentration of salts in closed basins such as the Tulare Lake basin in the Central Valley.In addition, some of the most productive soils in California such as in the western San Joaquin Valley originate from ocean sediments that are naturally high in salts.Irrigation water dissolves that salt and moves it downstream or it isThe salinity in the Colorado river used for irrigation in the Imperial Valley is higher than that of surface water from the snow melt.Although salinity problems can be found in various locations around California as shown in Fig.22, historically the major salinity issues are found in the Western San Joaquin Valley and the Imperial Valley.A thorough review of the history of irrigation in California was presented by Oster and Wichelns.Today, California’s interconnected water system irrigates over 3.4 Mha of farmland.The Imperial Valley in southern California has experienced salinity problems for many decades, since the Colorado river was tapped for irrigation in the early 1900s.By 1918 salinity had forced approximately 20,234 ha out of production and damaged thousands more hectares.The rapidly deteriorating agricultural lands from salinization forced the Imperial irrigation District to construct open ditch drainage channels.However, due to high salinity in the Colorado river water, heavy soils and poor on-farm water management at the time, the drainage system did not prevent continued salinization of the Imperial Valley.To address the problem, partnerships between the federal government, and the Imperial irrigation district were formed in the early 1940s that resulted in installation of underground concrete and tile drainage on thousands of hectares of farms.The subsurface drainage system and improved on-farm water management led to a reduction in the rate of soil salinization, resulting in flourishing agricultural production in the Imperial Valley.The water from the subsurface drainage tiles was routed to the Salton Sea.However, agricultural runoff and drainage flows with high salt content have affected the elevation of Salton Sea and increased its salinity threatening various wildlife species.On the positive side, the salinity load coming into the Imperial Valley as measured by salinity levels at the Imperial dam have not increased as previously projected.A report from the US Bureau of Reclamation reported a flow weighted salinity of 680 mg/L in 2011 at the imperial dam and had remained constant for past decades.Another major region in California significantly impacted by salinity is the western San Joaquin Valley , comprising the southern half of the Central Valley.From the second half of the 19th century to the early 1900s the SJV experienced rapid development of irrigated agriculture, along with it came drainage and salinity problems.The salinity problems on the West side of the valley can be attributed to high water tables near the valley trough caused by an expansion of irrigated agriculture upslope from the valley,soils on the West side are derived from alluvium originating from coastal mountains and other marine environments, and degradation of water quality in the San Joaquin river.In 1951, some of the fresh water in the San Joaquin river was diverted to irrigate agricultural lands on the east side north of Friant dam.The diverted water was replaced with saltier water from the Central Valley project.These changes coupled with agricultural return flows led to increased salinity downstream of the San Joaquin river, the main conduit draining the valley.

They have been successfully used in orchards, vineyards, and vegetable crops in many regions around the world with salinity problems, including Australia, Israel, California, Spain, and China.They are well suited because of their use of high frequency irrigation, thereby preventing dry soil conditions so that soil solution salinities remain close to that of the irrigation water, especially in the vicinity of the emitters where root density is highest.The salt distribution that develops around a micro-irrigation system depends on system type, but typically salts concentrate on the periphery of the wetted bulb for a surface drip irrigation, whereas salt concentrations typically increase with soil depth for sprinkler systems.The upwards capillary movement of water from the wetted soil depth near the subsurface drip emitter results in soil surface salt accumulation as water is lost through root water uptake and soil evaporation.For conditions where seasonal rainfall is inadequate to push those salts near the soil surface further down, options include preseason flood irrigation or sprinkling, moving drip lines every so many years when replacing or change crop rows between seasons.However, anecdotal evidence in the San Joaquin valley orchards has shown that salinity around drip irrigation systems can limit the volume of the root zone thereby limiting nutrient uptake, particularly nitrogen.The residual nitrogen ends up being leached to groundwater either by excess irrigation or winter recharge causing environmental degradation of groundwater quality.The complex interactions between soil salinity stress and water and nitrate applications were discussed in a model simulation study by Vaughan and Letey.

Libutti and Monteleone suggested that since soil salinity management is bound to increase the leaching of N,hydroponic net pots best practices should optimize the volume of water needed to reduce salinity and that required to avoid or minimize NO3 contamination of groundwater.They suggested to “decouple” irrigation and fertigation.Abating this salinity-N paradox with coupled nutrient-salt management will requires site specific considerations.Because of the potentially high control of irrigation amount and timing, it has been shown by Hanson et al., that subsurface drip directly below the plant row can effectively be used for irrigation under shallow water table conditions as long as the groundwater salinity is low.They showed that converting from furrow or sprinkler to subsurface drip is economically attractive and can achieve adequate salinity control through localized leaching for moderately salt-sensitive crops such as processing tomatoes, eliminating the need for drainage water disposal if so relevant.Controlled drainage —Whereas conventionally drains are installed in conjunction with irrigation systems in arid regions, controlled drainage systems originate in humid regions by control of the field water table using more shallow depth drainage laterals and control structures in the drainage ditches or sumps.In controlled drainage systems, irrigation and drainage are part of an integrated water management system where the drainage system controls the flow and water table depth in response to irrigation.Depending on objectives of the CD system, it can reduce deep percolation and nitrate concentrations in drainage water, augment crop water needs by shallow groundwater contribution, and reduce drainage water volume and salt loads for disposal.

Use of marginal waters—When freshwater resources are limited, salt tolerant crops can be irrigated with more saline water to be reused, for example by treated wastewater or drainage water.Management options include to apply irrigation water that is a mixture of saline with fresh water or cycle saline water with fresh water depending on growth stage , by using crop rotations between salt sensitive and salt tolerant crops, depending on when more saline water is available or through the use of sequential cropping as described in Ayars and Soppe.In addition to reducing freshwater requirements, it decreases the volume of drainage water required for disposal or treatment.A series of articles that present use of marginal waters has been edited by Ragab.In general, research results in this issue demonstrate that waters of much poorer quality than those usually classified as “suitable for irrigation” can, in fact, be used effectively for the growing of selected crops under a proper integrated management system, as long as there are opportunities for leaching to prevent detrimental effects, such as by sodicity.Studies have shown that drip irrigation gives the greatest advantages, whereas sprinkling may cause leaf burn.Cycling strategies are generally preferred, but beneficial effects decreased under DI.In addition, blending does not require added infrastructure for mixing the different water supplies in the desired proportions.Precision agriculture is increasingly becoming an established farming practice that optimizes crop inputs by striving for maximum efficiencies of those inputs thus increasing profitability while at the same time reducing the environmental footprint of those improved practices.While farming has always been about maximizing yield and optimizing profitability, precision farming has allowed for differential application of crop inputs across the farmer’s field, leading to more sustainable management.PA became possible through the broad availability of global positioning system and geographical information system technologies with satellite imagery in the 1980s.

It was focused on achieving maximum yields, despite spatial variations in soil characteristics across agricultural fields.It enabled farmers to vary fertilizer rates across the field, guided by grid or zone sampling.Therefore, inherent to precision agriculture is the use and refinement of the field soil map, in combination with soil and/or plant sensors.Whereas early PA applications depended solely on the soil map and its refinement, more sophisticated approaches have been introduced because of the parallel development of on-the-go sensor technologies, allowing for real-time soil and/or plant monitoring during the growing season thus expanding PA toward spatio-temporal applications.For a review of a broad range of such on-the-go-sensors, we refer to Adamchuk et al., including electrical/electromagnetic and electrochemical sensors for soil salinity and sodium concentration measurements.Whereas specific electrode sensors are available to measure Na concentration in soil solution, most of the EM sensors were developed to indirectly measure soil moisture by correcting for salinity interference, or to measure bulk soil ECb.The sole exception is the porous matrix sensor that was originally designed by Richards and reviewed by Corwin, measuring directly the electrical conductivity of in-situ soil pore water through an electrical circuit with the electrodes embedded in a small porous ceramic element that is inserted in the soil.The EC measurement is solely a function of the solution salinity because the air entry value of the ceramic is such that it will not desaturate beyond 1 bar.Corrections are required for temperature and response time for ions to diffuse from the soil solution into the ceramic.In their synthesis of high priority research issues in PA, McBratney et al.addressed the need to consider temporal variations, as yields typically vary from year to year.For irrigation applications, knowledge of within season variations are critical for BMP’s that minimize crop water and salinity stress.This has led to the term and application of Precision Irrigation, adhering to the definition of PA but applied to irrigation practices.Whereas traditional irrigation management strives for uniform irrigation across the irrigated field, it is the goal of PI to apply water differentially across the field to account for spatial variation of soil properties and crop needs, thus to also minimize adverse environmental impacts and maximize efficiencies.Moreover, PI advances allows for temporal adjustments of irrigation during the growing season because of changing weather conditions,blueberry grow pot including accounting for rainfall.PI can adjust water/ fertilizer amounts because of differential tree/crop needs , by controlling both application rate and timing at the individual tree/crop level or for larger management units.PI uses a whole-systems approach, with the goal to apply irrigation water and fertilizers using the optimal combination of crop, water, and nutrient management practices.As defined by Smith and Baillie , precision irrigation meets multiple objectives of input use efficiency, reducing environmental impacts, and increasing farm profits and product quality.

It is an irrigation management approach that includes four essential steps of data acquisition, interpretation, automation/control and evaluation.Typically, data acquisition is achieved by sensor technologies, while data interpretation would occur by evaluating simulation model outcomes, e.g.of crop response and salt leaching.Control is achieved by automatic controllers of the irrigation application system using information from both the sensors and simulation models, whereas evaluation closes the loop through adjusting the PI system.In addition to electrochemical sensors such as specific electrodes, optical reflectance devices such as near- and mid-infrared spectroscopy methods have been developed to quantify specific soil ion concentrations, particularly soil nitrate content.Over the past 20 years or so, many new soil moisture and salinity sensors have come to market, most of them being able to be included in wireless data acquisition networks.Selected reviews and sensor comparisons include Robinson et al.and Sevostianova et al..Shahid et al.showed the field results of a real-time automated soil salinity monitoring and data logging system, tested at the ICBA Dubai Center for Biosaline Agriculture.Recently there has been increased use of geophysical techniques for delineation of PI irrigation zones and for in-season irrigation and soil salinity management.For example, Foley et al.demonstrated the potential of using ERT and EM38 geophysical methods for measuring soil water and soil salinity in clay soils although they emphasized the need for calibration.Whereas traditionally, one would consider only drip or micro-sprinkler irrigation as a PI method, the broader definition can apply to most pressurized irrigation methods.Specifically, Variable Rate Irrigation is applied to center pivot, lateral move, and solid set systems, as reviewed recently by O’Shaughnessy et al..Many of the aspects of PI equally apply to such sprinkler systems, however, it is noted that their inherent complexity has precluded the required development of user-friendly interfaces for decision support, lagging the engineering technology.Specifically, the need to fuse GIS, remote sensing, and other temporal information with the DSS, allowing management zones to change over the growing season.Recent evaluations on impacts of using VRI on crop yield, water productivity were presented by Barker et al.and Kisekka et al., showing potential improvements when using VRI or MDI , but that additional research is strongly advocated especially because of the significant increased investments required.Another limitation to date of adoption of PI is that large-scale VRI systems require many sensors which can be cost-prohibitive, whereas determining their placement and number of sensors needed is not straightforward.It is worth noting that PI can also be applied to surface irrigation systems as described in Smith and Baillie.For example, automated gates coupled with SCADA systems and real-time data analytics can be used to optimize flow rates, and advances times to ensure infiltration rates match variable soil conditions.The application of PI to maintain plant-tolerable soil salinity levels was introduced by Raine et al., identifying research priorities at the time that allows for PI to be effective and pointing out that the level of precision, water application uniformity and efficiencies of most irrigation practices is sub-optimal.Among identified knowledge gaps was the lack of agreement between field and model-simulated data, especially for multidimensional model applications such as required for drip irrigation and for spatially-variable salt and water distributions at the individual plant root zone scale.This puts into question the usefulness of computer modeling for soil salinity management purposes, especially if there is general absence of soil salinity measurements to validate model simulations.Another limitation of successful PI is the lack of information on crop root response to salinity when considering the whole rooting zone in multiple dimensions as well as on crop growth stage.A central component of a road map toward precision irrigation is moving from a single management point within an agricultural field toward defining management zones across the field and eventually close to a plant-by-plant level of resolution were appropriate.It requires cost-effective sensors, wireless sensing and control networks, automatic valve control hardware and software, real-time data analytics and simulation modeling, and a user friendly and visual decision support system.Many sensor types and technologies are being developed and are introduced for soil moisture sensing; however, few applications include soil salinity sensing in concert with soil moisture monitoring.For PI to advance further, there is great need for much improved and cost-effective multi-sensor platforms that combine measurements of soil salinity with soil moisture and nitrate concentration.For a recent review of contemporary wireless networks and data transfer methods, we refer to Ekanayake and Hedley , that includes the use of cloud-based databases with smart phone apps and web pages.

Zooplankton were collected from the Bridge Tender Marina in Wilmington, North Carolina , using a plankton net . Samples were diluted in whole seawater, aerated, and used within 12 hours of collection. Under a dissecting microscope, individual calanoid copepods were selected using Pasteur pipettes and placed in beakers with bottoms made of Nitex mesh that were submerged in filtered and UV-treated seawater. Before experiments, copepods were dyed red to make the organisms easy to visualize in videos. To dye the plankton, the mesh beaker was submerged in a solution of Neutral Red for 20 minutes .To test the effect of copepod shape and drag without swimming behavior, dead copepods were used as prey. The copepods were selected and dyed as described above, then heat-shocked. To compare copepod swimming behavior with a smaller prey that does not escape, nauplii of Artemia spp. were hatched from frozen cysts by placing cysts in aerated, filtered seawater. Nauplii between 2-3 days old were selected using Pasteur pipettes, were housed in mesh bottomed beakers, and underwent the same dye treatment as the copepods.In some cases prey were captured on the far side of the observed tentacles. If a prey carried in the flow “disappeared” behind an illuminated tentacle and did not re-emerge, we assumed that it was captured. When this occurred, the tentacles were observed carefully in subsequent frames of the video and in every case the captured plankton became visible when the tentacles moved,hydroponic bucket the prey fluttered into view during peak velocities, or the prey washed off the tentacles.

In addition, aerial-view photos of each sea anemone in still water were taken directly after the experiment and captured plankton were noted. No discrepancies occurred between the total number of captured prey counted by the end of the experiment and prey observed on the tentacles once the experiment was complete. Predator-prey interactions were identified by the behavior of the prey . “Pass” described when prey passively swept by the anemone within the capture zone. “Avoid” described when a copepod actively changed trajectory with an escape jump to avoid contact with the predator . A “bump” described when prey passively bumped into a tentacle but continued without a capture or escape. “Escape” described when a copepod bumped into a tentacle then actively swam off . “Capture” described when prey bumped into a tentacle and was held by the anemone. Importantly, captured prey did not always lead to retention , so a final term “loss” was used to describe when prey would dislodge from the tentacle. The interactions “bump” and “escape” do not result in a capture so “loss” only refers to prey removed after a capture. The rates of predator-prey interactions were used to calculate efficiency. In Chapter 2, capture and trapping efficiency were calculated based on the proportion of encountered prey so that these values could be compared between predators with different feeding modes. In this Chapter, “retention efficiency” is defined as the proportion of captured prey that was retained so that we could compare the ability of the predator to hold onto prey that have different swimming behaviors. Since the duration of experiments was short relative to the average ingestion times for sea anemones , most captured and retained prey were not ingested during the videos. Therefore, the retention efficiency for sea anemones feeding on different prey alludes to feeding success but is not a confirmed measure of how much the predators consumed. Most of the zooplankton prey passed through the capture zone of a sea anemone without contacting the predator .

In weak waves, prey passively bumped into the predator, although live copepods came into brief contact with a sea anemone less than nauplii or dead copepods. In strong waves, the proportion of “bump” interactions increased for all prey types. Living copepods were able to avoid or escape the predator more in weak waves than in strong waves, but this difference was not significant. Nauplii and dead copepods do not actively avoid or escape from predators. Yet the proportion of predator-prey interactions that resulted in capture did not vary with exposure to stronger waves.The largest proportion of prey pass near the sea anemone without reacting . When solitary sea anemones preyed upon copepods, the prey avoided or escaped the predator more in weak waves than in strong waves. With a downstream predator, prey avoidance and escape swimming occurred less than in the same flow over solitary sea anemones, and increased in stronger waves, though not significantly . Predator-prey interactions between copepods and solitary sea anemones in still water were included to compare whether the differences in behavior over downstream sea anemones was due to slower flow conditions. In still water, the proportion of prey avoidance and escape responses were also low and increased as flow increased . The proportion of prey captured is not significantly different between solitary or downstream copepods, nor is it affected by increases in flow. Many studies of benthic suspension feeders test the effect of flow on feeding rate by animals in unidirectional flow with passive and uniform prey . Encounter rates increase with water velocity, which leads to higher ingestion rates. In this study, stronger waves led to increased encounter rates only for passive particles, such as dead copepods . For prey that swim and perform escape maneuvers, stronger waves did not significantly enhance encounter rates. In weak waves, sea anemones encountered copepod prey at higher rates than nauplii and dead copepods, which suggests prey swimming behavior affects variability of encounter rates.

The differences in how flow affected encounter rates for three prey types were not mirrored in capture or retention rates. For passive prey, more encounter rates with a benthic predator did not result in greater rates of capture. Copepods in weak waves encountered a predator at a higher rate than nauplii, but capture rates were similar, which indicates that the capture and subsequent retention of prey does not scale equally from encounter rates for prey with different behavior. Importantly, retention rates were low for both nauplii and copepods in both weak and strong flow regimes. Dead copepods represented the extreme range of retention rates since these prey were retained at high rates in weak waves, but were not retained at all in strong waves. The comparisons between rates of encounter and capture for prey with different swimming behavior suggests the importance of evasive responses in avoiding contact with a predator,stackable planters reducing passive bumps into predators, and jumping free after getting captured. The proportion of predator-prey interactions between nauplii and dead copepods were similar . Copepod avoidance might have reduced passive bumping into predators in weak waves, but the proportion of capture remained the same in weak and strong waves. Downstream sea anemones encountered fewer prey than solitary sea anemones. Upstream neighbors can deplete water of prey as flow passes over the clone. The encounter, capture, or retention of prey by downstream sea anemones was independent of flow. Although these predators encountered fewer prey than solitary sea anemones, they retained approximately the same rate of prey. For benthic suspension feeders, turbulent and wavy flow enhanced encounter rates for passive prey but not for prey with active swimming behavior. Higher encounter rates of passive prey did not result in higher capture or retention rates. Similarly, feeding in the presence of neighbors lowers encounter rates but retention efficiency remains the same in weak and strong wakes. This study highlights the use of realistic flow conditions, prey with swimming behavior, and in the presence of neighbors to examine passive suspension feeding in benthic organisms. Soil is vital to humankind and our livelihood.Soil processes affect the quality of the food we eat, the water we drink, the air we breathe, and is the foundation of our living and transportation infrastructures.As the world’s population continues to grow and society expects a wider range of food selections, to provide this more selective world with nutritious food and feed will largely depend on our ability to maintain and sustain productive agricultural soils.Recognizing that soils have a central place in achieving food security, we note that the available arable land resource is decreasing at an alarming pace.In fact, we are at a point in time of what could be designated as a decade of peak agricultural land globally, indicating that the world’s area of productive arable land is nearing its maximum.This is so because the annual expansion rate of new farmland is becoming less than the land area removed from agriculture.Causes for reduction in productive farmland are its conversion to urban and industrial development,taken out of production because of it being degraded such as by soil erosion, compaction or salinization, and threatening public health because of soil contamination.It is estimated that about 15% of the world’s total land area has been degraded.In addition to the acreage of productive agricultural land decreasing, freshwater resources are also becoming scarce as populations increase, demanding additional water for domestic and industrial use.

Moreover, while diverting increasing volumes of water for maintaining healthy freshwater environments and ecosystems, water for irrigated agriculture is becoming restricted in many arid and semi-arid regions.We note that whereas only about 15% of the world’s agricultural land is irrigated, it produces about 45% of global food production and even more for fruit and vegetables.As high-quality freshwater availability is becoming a major constraint globally, increasing water use efficiency of irrigated agriculture is becoming essential.This form of agricultural intensification means to do more with less while simultaneously minimizing its environmental footprint and mitigating its contributions to climatic changes and/or adapting to it.Additional constraints on agricultural production include public debates and policy changes regarding its environmental impacts on soil, air, and water quality, the use of genetically modified foods, as well as the threat of a changing climate.Among various mitigation and adaptation options, one calls for sustainable intensification of agriculture, water- and climate-smart agricultural practices, as well as for conservation agriculture to improve soil health and to minimize environmental impacts on soil, water, and air quality.In addition, other non-soil related practices are suggested, such as closing crop yield and nutrient gaps and reducing food waste.Collectively, any of these land and water management practices serve to enhance soil quality, reduce the environmental footprint, conserve freshwater resources, reduce soil degradation while sustaining food production.Hence, the preservation of our soils is crucial.It is no wonder then that we must address causal factors of soil degradation, such as by water and wind erosion, soil contamination and soil salinity.We note that the room to expand cropland beyond the estimated 12% of the terrestrial land surface is limited, because most productive lands are already in agricultural use, whereas converting additional land would lead to either increasing environmental impacts of marginal lands or destruction of the world’s richest natural ecosystems.The importance of sustainable land management was recently acknowledged in the IPCC.Special Report on Climate and Land , highlighting interactions and feed backs between our changing climate, land degradation, sustainable land management and food security, stating: “Land provides the principal basis for human livelihoods and well-being including the supply of food, freshwater and multiple other ecosystem services, as well as biodiversity.Human use directly affects more than 70%of the global, ice free land surface.Land also plays an important role in the climate system.” Among the most prevalent forms of soil degradation, in addition to air and water erosion and soil contamination, is human-induced soil salinization.Soil salinization occurs by the accumulation of water-soluble salts in the plant rooting zone, thereby impacting water and soil quality, and inhibiting plant growth.Osmotic changes in soil water caused by total salinity reduce the ability of plants to take up water from the soil.In addition, specific ions such as Na and Cl negatively impact plant physiology and become toxic when absorbed by the plant at higher than beneficial amounts.Besides, Na accumulation in surface clay-mineral soils cause soil swelling and dispersion thereby reducing water infiltration and soil drainage and causing water logging and flooding in sodic soils.The geological salinization is by far the largest fraction of the approximately 1 billion haof salinized land, making up about 7% of the earth’s land surface.In addition, approximately one-third of the world’s irrigated land is salt-affected in some way , equal to about 70Mha.

Emergent technologies and methods are also applied to these questions, such as “advances in geometry, graph theory, topology, control theory for chaotic systems, and novel approaches for managing and modeling uncertainty.” Mathematics, they said, is considered the most fundamental language for an understanding of “biocomplex systems.” As Anna Tsing writes, “The common assumption is that everything can be quantified and located as an element of a system of feedback and flow.” One research program that successfully met the NSF’s biocomplexity funding criteria in 2000 was the Bahamas Biocomplexity Project , a large multi-year proposal that situated itself as a mediator between two institutional milieus. The first was that of the NSF’s biocomplexity research program, as just described, with its concerns with interdisciplinarity and the production of more socially robust and politically relevant knowledge. The second was the ongoing and highly political marine conservation scene in the Bahamas at that time, which I will describe. I hope to highlight one of the ways in which scientific research practices manipulated and produced their own social reality in order to create the commensurable information required by the BBP. In 2000, the Bahamian government announced its political intention to create a Marine Reserve Network , which would initially include five protected areas within the borders of the archipelagic nation. These areas, following the trends in international conservation science,gutter berries were to be designated as “no-take” reserves, areas in which the extraction of any form of marine resources is prohibited, and they were a response to the concern over perceived environmental degradation.

The announcement of the MRN project came after two years of planning meetings and negotiation sessions between the Bahamas Department of Fisheries, now Marine Resources, and environmental non-governmental organizations , including the Bahamas Reef Environmental Education Foundation and the Nature Conservancy of the Bahamas , who fear that sustained over-fishing is leading to the destruction of the Bahamian coral reef system, biodiversity loss, declines in fisheries productivity, and who predict that the Bahamas will go the way of the rest of the Caribbean and lose species diversity and valuable commercial fish stocks. The proposed reserves are located near the clusters called the Berry Islands, the Exuma Islands, the Bimini Islands, and the larger islands of Abaco and Eleuthera and were thought up largely as a response to the declining populations of Nassau Grouper, Caribbean Spiny Lobster, and Queen Conch, the primary commercial species in the region, described as the Bahamian “holy trinity.”The BBP, a loose entity made up of researchers from fields including anthropology, biology, oceanography, physics, economics, and mathematics, stepped into this scene to conduct long-term, multi-phase research on these proposed marine reserves, their feasibility, and subsequent systemic effects to produce policy recommendations for the Bahamian government as well as detailed and predictive models of coral reef functioning that could possibly be transferred for the management of other reef systems. The “Social Working Group,” lead by an environmental anthropologist and an environmental economist, was supposed to go about “assessing patterns of resource use and attitudes about resource conservation among stakeholders,” using survey technologies to compile comparable data sets from communities situated near proposed reserve areas or those identified as having an economic reliance on fishing.

Anthropology, as a discipline representing the behavioral sciences, was enlisted here in order to make sure that the knowledge produced for the modeling project reflected the cultural reality of the Bahamas. Anthropology was seen as the disciplinary voice of the local, as the discipline that would legitimate claims to social truths made by the BBP.The findings of the Social Working Group have been recently collated, summarized, and published separately from the other BBP working group results and projects in an article that stresses the necessity of socioeconomic assessment as an aspect of environmental management.The authors, Broad and Sanchirico, focus their analytic attentions on the quantification of what they describe as socioeconomic variables and environmental perceptions of individuals and communities that have been gleaned from the fieldwork. Variables, for these social scientists, are those traits that can be pinned to particular individual or community entities and then compared across a number of individuals or within communities. They assessed specific variables found within the completed fieldwork data, such as the “demographic variables” of individuals surveyed, i.e. their age, number of children, level of education, marriage status, gender, occupation as either in tourism, fishing, or other, household income, if the mother was from the specific settlement, if past generations of their family had been occupational resource users like fishermen or farmers, if they had heard of marine reserves or been to a reserve meeting, and how frequently they went to the sea to use marine resources. These variables were calculated for five particular communities, identified as small islands or specific settlements on larger islands, and in total across all 485 survey participants. Perceptions are also understood here as variables, but they are variables that pertain to participant’s responses to particular management oriented ideas around “environmental conditions” such as the state of local marine conditions, the level of threat to the marine environment, and the state of the enforcement of fishing regulations. These “perceptions” where then paired with variables such as the participant’s household income, fishing reliance, tourism reliance, and whether they thought there should be a local marine reserve put in place in the area.

The demographic variables are described as concrete “material aspects of life” while the perception variables are described as individual and community “perspectives.” When statistically linked, the material aspects of life can be shown to have more or less influence on a certain perspective in a certain place, and this data,strawberry gutter system when collated for specific communities, can become a management tool.The BBP is a prime example of ways in which “the social” becomes implicated in contemporary conservation science projects in the living laboratory of The Bahamas and elsewhere. It is my contention that in order for an increasingly necessary sociality to become scientifically implicated in the production of such peculiar politics, it must first be assessed and formalized, which implies that it must be conceptually formed and designed- that is, made assessable in the first place. The development and deployment of the BBP’s social science survey and the results gleaned from the data demonstrates the potential possibilities and pitfalls of this work. Based largely on my strange experiences with the project, I have come to see the socioeconomic survey as a powerful example of the way in which biocomplexity research activated certain instrumental notions of individuality and community as sociality bolstered by a certain notion of anthropology.The survey itself was concerned with statistically elucidating the connection between prevailing local economic conditions in an area and the variety and intensity of marine resource extraction conducted by individuals within that area as well as what they thought about the appropriateness of such extraction- all part of what the project refers to as “human and environmental interaction,” mentioned above. One of the defining features of the survey’s demographic variables is the categorization of each person interviewed by their current occupation, with a focus on either tourism or fishing, and the occupational history of their parents and grandparents,with a focus on “resource use.” Following Julia Paley, this can be thought of as an articulation of subjectivity, activated in spatial and temporal frames, wherein occupation is tied to particular extractive activities, appearing later in the survey, involving notions of self-interest centered around livelihood.These interested notions are productive of idioms of person hood based on an assumption that individuals have rights and claims to extract value from the material environment, and that the form these claims to value take represents what distinguishes one person from the next and one settlement from the next in terms of perspective and perception.

In the language of conservation and development, people making similar claims- having similar perceptions linked to specific variables- can then be lumped into stakeholder groups, and these groups then become instrumentalized actors- or, in the case of the BBP, groups based on occupational interest create the category “commercial fisher” or “tourist employee,” and groups based on location become “communities” which have their own distinctive traits depending on the stakeholder groups within them. These groups are made distinctive and therefore amenable to targeted management. Following Hayden, I would like to point out that it is not the identification of interests which explain social processes- i.e. the explanation that fishermen have particular interests in marine resources- rather, it is the analytic assembly of interests, values, and interested persons that is itself processual and worthy of study.Thinking in this manner allows the analytical focus to come off of assessing the extractive traits of those who fall within a given occupational category or who manifest a predetermined variable, and shifts it to the consideration of the work such notions do for those who would deploy them, such as the social scientists of the BBP. Interest, value, and variables then become ethnographic objects. Such a focus helps demonstrate that “there can be no production of value without processes of subject formation,” and the persons and communities defined by occupation produced by the BBP demonstrate the instrumental creation of a realm of inclusion and exclusion dictating the ways in which people are recognized and assessed within a particular paradigm, in this case nascent biocomplexity research.The socioeconomic surveys employed by the BBP, rooted as they are within a particular logic, instrumentalize and activate particular figures of the local, rural, and of the Out Islands, usually in occupationally evaluative terms and variables that come to stand for a sort of person hood. Fisherman becomes an occupational category that signifies particular extractive activities for self-interested gain and claims to tradition, lineage, and subsistence, all accumulations of value, which are different from activities connected to the category of tourism employee. Tourism and fishing have become construed here as existing in an inverted relationship, with fishermen hypothesized to be less likely to support marine reserve creation and tourism employees more likely, based on what are described as different forms of interaction with the marine environment which are linked to diametrically opposed perceptions of that environment and what to do with it. Further, when and if the individual survey results are statistically aggregated and linked to the other forms of BBP research, community and locality may become reactivated as sites which also have a self-interested nature and attendant claims and rights to accumulate value. To evoke Julia Paley again, statistics becomes a tool for social diagnosis, wherein research subjects become the object of study and are prevented from acting as authors- their participation becomes drastically proscribed. Interviewers, such as myself, who struggle to fit the given answers to survey questions into the format of the survey mode of information in order to create variables, also become produced as objects of the survey, standing in as representatives of the double legitimacy of anthropological social research and the transparency of the survey method itself. The Social Working Group and its publications are part of the orchestration of socially robust knowledge that comes with contemporary environmental management practices.The sociality of the research must be demonstrated, as Strathern would say, and it must be stabilized. What has been produced here by the BBP is a socioeconomic assessment which does this work of stabilization and demonstration in order to make Bahamian social forms which are manageable and an environmental management apparatus which has socially responsible options. As a participant myself in this social scientific design project, I wonder about the possibilities for targeted management mentioned by Broad and Sanchirico. It is one thing to show that there are a diversity of perspectives held by rural Bahamians about the marine environment and that management should recognize this diversity, as these authors argue, but it is quite another to make this diversity demonstrable, numerical, and localized- to operationalize constructed variables and orchestrate this data into a tool for targeting specific groups and communities for conservation education, economic development based in ecotourism, and various other forms of environmental management.simultaneously abstract and material, that ecological, biological, and conservation scientists and managers variously do. This work influences the way that the world is perceived, how new kinds of relations are formed, how futures are imagined, and what should be done about it all.

These combinations may be capable of activating specific pathways to differing degrees to achieve pathogen appropriate defense responses. Such stimulators of the plant’s inherent immune responses are likely to be superior to conventional biocidal pesticides that are harmful to both environment and consumers . Knoth et al., previously identified two different synthetic elicitors, DCA and CMP442 – thiazolidine-4-carboxylic acid. Both elicitors induce defense in Arabidopsis against Hpa and DCA also against P. syringae. The modes of action of these compounds are distinct; although both act on the SA-dependent branch of the defense network. CMP442 appears to interfere with defense-signaling processes upstream from SA perception, while DCA activates signaling steps downstream from SA . This screening system focused on compounds targeting components of the SA-dependent sector of the defense network and yielded many candidate synthetic elicitors . To widen the spectrum of functionally distinct synthetic elicitors a screening system was needed that allows for the identification of synthetic elicitors interfering with the JA- and ET-dependent parts of the defense signaling network. A set of five genes was identified in microarray experiments that exhibit SA-independent upregulation in response to infection with Hpa . Four of these genes were members of the PDF family including JA-pathway marker gene PDF1.2b. Because PDF genes are known to response to JA and ET, but not SA,ebb and flow table this set of co-expressed defense-related genes was named JEDI and include PDF1.2a , PDF1.2b , PDF1.2c , PDF1.3 , and JEDI1 .

Here the development of transgenic lines in which select JEDI genes were fused to reporter genes to develop a high-throughput chemical screening system is described. In addition, the creation of transgenic plants with an RNAi transgene silencing transcripts of the closely related PDF members within the JEDI set is reported. Furthermore, JEDI transcripts were hyper induced at 48 hpi in nahG compared to Col-0 . The Hpa-inducibility of the JEDI transcripts was confirmed via reverse transcription -PCRs at 0, 6, and 12 hpi with HpaEmoy2 in two-week-old Col-0 and nahG plants. Compared to their levels at 0 hpi, transcript levels of all JEDI genes were enhanced at 6 hpi and 12 hpi in both Arabidopsis lines. Thus, the trends observed in these RT-PCRs were similar to those in the original microarray data, suggesting that JEDI transcript accumulation in response to HpaEmoy2 recognition is at least partly SA independent. Additional time points were examined after Hpa in Col-0 and nahG.PDF genes are known to be positively controlled by the JA-dependent branch of the plant defense network. However, JA-controlled defense responses have been traditionally associated with immunity against necrotrophic or hemibiotrophic pathogens, such as the fungus B. cinerea or the bacterial pathogen P. syringae . Immunity against strict biotrophs, such as Hpa is believed to be controlled by SA dependent immune responses . However, our observation that JEDI–PDF genes are upregulated during incompatible Hpa interactions suggested that JA-dependent signaling processes can also contribute to immunity to this strictly biotrophic pathogen. Thus, this set of Hpa-responsive genes provided us with an opportunity to study aspects of JA-dependent processes in immunity against Hpa. In order to design a high-throughput screening protocol for the identification of synthetic elicitors targeting the JA-dependent branch of the plant defense network, a previously characterized pPDF1.2b::GUS line was obtained and tested.

Seven-day-old seedlings were grown in liquid growth medium in 96-well plates and incubated for 24 h with 100 µM , 45 µM , or mock solution . A concentration of 45 µM MeJA induces expression of pPDF1.2b::GUS . SA should not induce this reporter . At 24 h after the respective treatments, seedlings were histochemically stained to visualize GUS expression .Even the mock-treatment resulted in GUS expression . Due to the apparent lack of specificity in expression responses a screen with this pPDF1.2b::GUS line, this screen was deemed unfeasible. Therefore, a set of new transgenic lines with fusions of JEDI promoters to reporter genes was developed and tested for their suitability for high-throughput chemical screens. Reporter lines ideal for the planned chemical screens should show no or extremely low background expression and exhibit clear pathogen or JA-inducibility. In addition, the variability of reporter gene expression levels in response to the same treatment should be minimal. A reduction in transcript levels of genes important for plant defense can affect R-gene-mediated resistance and/or basal defense responses. A reduction in basal defense may result in enhanced susceptibility to virulent pathogens . To identify effects on basal defense, the homozygous PDF-RNAi lines were infected with the Col-0 virulent Hpa isolateNoco2 . The interaction of HpaNoco2 with Col-0 is compatible, as this Hpa isolate is not recognized by any Col-0 R gene . Three-week-old plants were spray-infected with 2 ml/pot and 7 days post inoculation the extent of spore formation was quantified. Homozygous PDF-RNAi lines 38, 41, and 48 were in the wrky70-3 background.

Lines were created in the wrky70-3 background to see if knocking down gene expression in this mutant line might display different results than in the Col-0 wild type line. PDF-RNAi lines transformed into the wrky70-3 background displayed similar levels of infection as wrky70-3. In addition, wrky70- 3 and its transgenic lines consistently supported similar levels of spores as Col-0. This is contrary to previously reported data, which demonstrated that wrky70-3 supported more pathogen growth than Col-0 . Experiments performed with Arabidopsis plants at a range of ages indicated that WRKY70 transcript levels are upregulated in an age-dependent manner . In two-week-old Arabidopsis plants WRKY70 transcript levels were lower than in three-week-old plants. While basal defense up to an age of two weeks seems to be dependent on WRKY70, this transcription factor seems not to be required for this immune response in older plants. No morphological abnormalities were apparent in any of the PDF-RNAi lines. Pathogen recognition triggers a highly intricate set of defense responses which are coordinated by a complex regulatory network . Two branches of this network, which are dependent on the signaling molecules SA or JA, respectively, have been previously characterized. In Arabidopsis, SA-dependent signaling can processes induce antimicrobial proteins . Alternately, induction of PDF genes such as PDF1.2 is dependent on JA-dependent regulatory processes. While SA-dependent plant immune response have been primarily associated with resistance against biotrophic pathogens, defense reactions promoted by JA seem mainly to be effective against necrotrophs . Extensive crosstalk between JA- and SA-signaling has been reported as both types of defense signaling processes can be additive, antagonistic,flood table or synergistic dependent on the extent of their induction . Furthermore, successful defense against certain pathogens or pests often requires the coordinated induction of both SA- and JA-dependent defense reactions . High-throughput chemical screens previously identified synthetic elicitors activating SA-dependent plant immune response . A complementary screen to identify synthetic elicitors stimulating JA-dependent defense signaling processes would have great potential for the further decipher plant defense networks and provide molecular probes to uncover crosstalk mechanisms coordinating SA- and JA-dependent defense reactions. Interestingly, in nahG Arabidopsis plants JEDI transcripts appeared to be hyper induced in response to infection by Hpa suggesting they are upregulated by signaling mechanisms normally antagonized or suppressed by SA. As the JEDI set includes several PDF genes which are known to be positively regulated by JA , the hyperinduction of JEDI transcripts in the nahG background may point to a JA-dependent gene induction mechanisms that is counteracted by SA. To decipher roles that the JEDI genes may play in defense and stress responses, publically available microarray data were examined. The expression profiles of PDF1.2a, PDF1.2b, and JEDI1 were available through the Botany Array Resource website . These genes were highly upregulated in response to the oomycete Phytophthora infestans, the fungi Erysiphe orontii, Botrytis cinerea as well the abiotic stimuli wounding, osmotic stress, ultra-violet light B treatment, oxidative stress, and drought.

Additional treatments reported on in BAR, such as: SA, the ET precursor 1-aminocyclopropane-1-carboxylic-acid, the cytokinin zeatin, methyl jasmonate, indole-3-acetic acid , abscisic acid , gibberellic acid , and heat caused no significant changes in the expression profiles of PDF1.2a, PDF1.2b, and JEDI1. Microarray data in the BAR database therefore indicated that a wide range of pathogens and stressors may induce JEDI expression. Wounding triggered the accumulation of JEDI transcripts . However, JEDI transcripts did not accumulate in response to treatment with MeJA . A likely explanation for this unexpected observation is that responses to MeJA were measured at early times after MeJA treatment. , while previous studies showed PDF transcripts to accumulate around 48 h after treatment with jasmonates . Microarray data sets in BAR include responses of Arabidopsis to different types of pathogens, such as the hemibiotrophic oomycete P. infestans, the biotrophic fungus E. orontii, and the necrotrophic fungus B. cinerea . Thus, transcriptome responses of Arabidopsis to a complete set of pathogenic lifestyles are represented in BAR. Of these three different types of pathogens, the hemibiotroph P. infestans induced the strongest accumulation of JEDI transcripts while the other two pathogens induced expression to a lesser degree.Besides canonical JA-response elements, additional putative cis-elements are commonly present in all PDF promoters. These include binding sites of the AP2-domain transcription factor RAV1, which binds to bipartite recognition sequence, one of which is a AP2 domain . GCC boxes are known to mediate responses to ET or JA . In addition, W-box motifs are present in JEDI promoters. W boxes have been mainly associated with SA-dependent regulatory mechanisms, but may have wider roles in defense gene regulation . Furthermore, GATA promoter, and I-box motifs are present JEDI1 and PDF1.2a suggesting that these genes have particularly diverse roles. GATA and I-boxes are light-responsive promoter elements. The JEDI genes also respond to light and many non-defense-related stimuli, which again suggest a diversity of roles for these genes. It has been previously reported that the GCC box is important, but not essential, for the defense-related up-regulation of PDF1.2b . Thus, additional promoter elements must also be involved in the defense-related up-regulation of PDF1.2b . While the created transgenic lines with pPDF::LUC or pPDF::GUS fusions seemed not suitable for new synthetic elicitor screens, as they exhibit high background expression levels, these lines may still be useful for other types of experiments. They can be used to study spatial and temporal patterns of pathogen-induced JEDI gene expression. They may also allow the rough localization of promoter elements mediating responses to various defense related stimuli, such as infection with virulent or avirulent Hpa isolates. The high degree of structural relatedness and similarities of their defense related expression among PDF genes suggested functional redundancy. Studies using single mutants for individual PDF genes have not been reported on in the literature for the defense related functions of these genes. Thus, only a quadruple mutant with combined mutations in each of the four PDF genes is likely to exhibit clear defense-related phenotypes. The construction if such a quadruple mutant, however, is not feasible due to the extremely close linkage of PDF1.3 and PDF1.2b as well as PDF1.2c and PDF1.2a . As the nucleotide sequences of these four PDF-JEDI genes share a high degree of identity, RNAi-based silencing using the pANDA-RNAi vector seemed a feasible strategy. Several Arabidopsis lines containing the PDF-RNAi vector exhibited reduced basal defense against Hpa. However, in these lines transcript levels of only PDF1.2c and PDF1.3 appeared to be reduced. Thus, co-silencing of these two PDF members may be sufficient to overcome functional redundancy within this group of defense genes. Unfortunately, the RT-PCR analyses measuring PDF transcript levels were not consistent. Measurements of the respective transcripts need to be repeated by a more reliable and robust method, such as real-time quantitative RT-PCR. Assays to examine the effect of RNAi-transgene on resistance to other pathogens should be also performed. In any case, this study, which demonstrates a potential role of some PDF genes in basal defense against Hpa indicates that members of this gene family can contribute to immunity against a strict biotroph. While this finding is novel, it is not unexpected, as PDF transcripts were found to accumulate during infections of Arabidopsis with pathogens of different lifestyles, including biotrophs .

Following the activation of initial and local defense responses are a set of delayed and systemic responses that include systemic acquired resistance . SAR is an induced form of defense that is activated remotely from the point of pathogen infection conferring a broad spectrum disease resistance against a variety of pathogens . Like many local defense responses, activation of SAR requires the accumulation of the signaling molecule salicylic acid . A complex regulatory network has been shown to be required for proper regulation of these plant immune responses . Many components of this network are commonly utilized by PTI, basal defense, ETI, and SAR. Major regulators of plant defense responses are protein kinases, which act at various hierarchical levels within the plant defense network . There are more than 1000 protein kinases in Arabidopsis . In particular, receptor protein kinases , Ca2+-dependent protein kinases and mitogen-activated protein kinases have been implicated in the regulation of plant immune responses . RPKs are comprised of a transmembrane domain with amino-terminal extracellular domains implicated in ligand recognition and protein–protein interactions, in addition to a carboxyl-terminal intracellular kinase domain involved in signal transduction . The three major sub-classes of RPKs are differentiated based upon their kinase domain substrate specificities. The sub-classes include: receptor-tyrosine kinases,grow bucket receptor-serine/threonine kinases, and receptor-histidine kinases .

Most plant RPKs are proteins containing an: extracellular signal sequence, extracellular leucine-rich repeats , a transmembrane helix, and cytoplasmic kinase domain with the serine/threonine consensus sequence . One variant in the RPK group is the receptor-like kinases , which belong to a large family known as the RLK/Pelle family. The Arabidopsis RLK family is divided into 45 subfamilies with over 600 members that comprise more than 2% of the Arabidopsis genome . One of the main criteria that distinguishes these subfamilies is the existence and type of extracellular domain . There are 15 classifications for RLK extracellular domains, which include: CRINKLY4-like, C-type lectin-like, CrRLK1-like, DUF26-like, extensin-like, legume -lectin-like, LRK10-like, LRR-like, LysM-like, PERK-like, RKF3-like, Sdomain-like, thaumatin-like, URK1- like, and WAK-like . The LRR domain is the most common and represents the largest RLK group with 216 members subdivided into 13 subfamilies . Most RLKs have a conserved arginine and an aspartate in the activation loop of subdomain VI, which acts as a kinase activator by enhancing phosphotransferase efficiency . Often kinases with arginine and aspartate are important for developmental regulation, while those without these conserved residues are important in innate immunity . Accordingly, plant RLKs can be further subdivided into two major categories based upon their functions: one is involved in cell growth and development and the other in plant–pathogen interactions and defense responses . Examples of this second group are PRRs: Xa21 from rice and FLS2 from Arabidopsis , which interact with certain MAMP-type epitopes. Xa21 is membrane bound serine/threonine protein that is activated by AxYS22, a 17- amino acid peptide conserved in strains of Xanthomonas.

FLS2 is a transmembrane protein that recognizes a number of bacterial MAMPs including peptides derived from the flagellin such as flg22 . Another RLK, CERK1, belongs to a distinct subfamily and is required for immune signaling triggered by fungal chitin. In addition, CERK1 binds and recognizes bacterial peptidoglycans contributing to immunity against bacteria . Another group of kinases important for defense are CDPKs, which are encoded by a 34-member gene family in Arabidopsis and make up one of the largest family of Ca2+ sensors in plants . Host proteins must be able to sense alterations in Ca2+ levels and respond accordingly . CDPKs have N-terminal protein serine/threonine kinase domains attached through an autoinhibitory junction domain to a C-terminal Ca2+-binding calmodulin-like domain . CDPKs bind Ca2+ at their C-terminal domain, which activates their protein kinase activity and facilitates their function as transducers of Ca2+signals. A possible role of Ca2+ in plant defense was proposed when CDPK transcripts were found to be elevated in tobacco, maize, tomato or pepper in response to pathogens or their elicitors . Upon pathogen recognition, cytosolic Ca2+ levels increase . The duration and amplitude of these increases are specific for the respective defense-related stimulus, resulting in the differential activation of downstream components . Two proteins have been suggested as potential substrates for CDPKs in plant defense: PAL and plasma membrane associated NADPH oxidase . PAL appears to be phosphorylated in bean cells challenged with a general elicitor but the significance of this observation remains to be demonstrated. In addition, a CDPK was shown to enhance NADPH oxidase activity stimulating an oxidative burst in tomato protoplasts although the significance of this interaction is also not clear . Romeis et al., demonstrated defense-associated activation of CDPKs in tobacco cell cultures transformed with the Cf-9 gene from tomato. Cf-9 is responsible for providing resistance to Cladosporium fulvum in the presence of its corresponding avirulence gene Avr9.

They established that the presence of Avr9 and Cf-9 a kinase was phosphorylated, causing an increase in kinase activity. They further demonstrated that this kinase is of the CDPK-type, because it required Ca2+ . This was the first direct demonstration of CDPK enzyme activity in plant defense. Meanwhile it has become clear that CDPKs are important not only in plant defense signaling but also serve as key points of convergence of various regulatory pathways due to their ability to respond to different hormonal or environmental cues . To better understand CDPK function in plant defense, additional pathogen-induced CDPK-phosphorylated substrates need to be identified. Mitogen-activated protein kinase cascades transmit and magnify signals through a phosphorelay mechanism involving: MAPK-kinase-kinases , MAPK-kinases , and MAPKs. They link upstream recognition events to downstream targets and their sequential phosphorylation targets substrate proteins in the cytoplasm or nucleus. MAPK activation is one of the earliest conserved signaling events after pathogen recognition . Many signaling cascades are shared between different activating stimuli . Cross-inhibition, feedback control, and the use of defined scaffolding proteins connecting distinct signaling components are utilized to enforce specific relationships between activating stimuli and the respective biological responses . Cross inhibition is manifested in the mutual inhibition between two pathways . Feedback control can be represented by negative feedback loops, where the activation of one component down-regulates the function of another. Scaffold proteins bring components together, which enhances specificity within signaling chains . Little is known about specific scaffolding proteins within plants. Two putative plant scaffolding proteins include alfalfa OMTK1, which interacts in protoplasts with the MAPK MMK3 in response to H2O2 and Arabidopsis MEKK1, which binds to MKK2 and MPK4 . MAPKs pathways are known to be involved in plant development, programmed cell death, responses to some abiotic stressors, and defense signaling. The Arabidopsis genome codes for 110 MAPK cascade components, which includes 20 MAPKs, ten MAPKKs and 80 MAPKKKs . Few MAPKs have been studied due to their lethal mutant phenotypes in plants . The most well understood MAPKs are MPK4, MPK3, and MPK6,dutch bucket for tomatoes with the latter two acting as positive regulators for defense responses and the former being a negative regulator of SAR. The Flg22 peptide is recognized by the receptor FLS2 which complexes with BRI1-ASSOCIATED KINASE and triggers MAPK signaling cascades. This cascade includes the activation of MPK3, MPK4 and MPK6 . MPK4 and MPK6 are also activated by hrp proteins from some bacteria and their activation results in the induction of PR genes which sometimes encode proteins with antimicrobial activities . Further studies must identify and elucidate MAPK cascades and find ways around the widespread mutant lethal phenotypes which inhibit kinase pathway studies. Traditional mutational analyses have been unable to circumvent functional redundancy and lethal mutant phenotypes . Thus, additional types of experimental approaches are necessary for the continued elucidation of the intricate and elaborate circuits within plant immune networks. One novel approach, chemical genetics, offers distinct advantages over traditional techniques.

Chemical genetics allows bioactive small molecules to be used in a reversible manner, since frequently their effects on organisms are not permanent. In addition, it provides more temporal control over experiments, since chemicals typically interfere with their targets immediately after application. In contrast, the timing of pathogen infections is often poorly reproducible, as the germination of spores or pathogen growth and spread in plants is asynchronous and often highly sensitive to subtle changes in environmental conditions. Chemicals also have the ability to simultaneously affect multiple members of highly-related protein families, permitting the study of biological functions of functionally redundant proteins. Using traditional genetics to knock out the function of an entire gene family often proves difficult or infeasible due to technical challenges and lethal phenotypes. Yet another advantage over traditional genetics is that bioactive chemicals allow for the study of essential gene functions at any stage in development because transiently active compounds can be added at any time or any concentration. In contrast, genetic mutations are of permanent nature. If they confer lethal phenotypes, no studies can be performed. Finally, the function of multiple structurally unrelated genes can be knocked out concurrently by using combinations of chemicals while also varying the concentration of each chemical allowing the study of quantitative relationships between defined stimuli and phenotypes . Chemical genomics requires tens of thousands or even hundreds of thousands of chemicals to be screened for their ability to stimulate a particular phenotype of interest . The increase in demand for chemicals that can manipulate a diverse set of biological processes resulted in the need for inexpensive large and structurally diverse chemical libraries for screening. As a result, the concept of combinatorial chemistry was developed . This high-throughput approach is based on simultaneously occurring synthesis steps. During each step a set of distinct chemical building blocks is used, yielding a vast number of structural combinations, referred to as “a combinatorial libraries”. The ease of this novel form of synthesis made these libraries widely available and cost-effective to many fields of academic research . Thus, the large sample size of available structurally distinct chemicals maximizes the probability that compounds will be identified that induces the desired biological effect. The Eulgem lab uses chemical genomics to identify and characterize synthetic elicitors, which are small drug-like molecules that induce plant defense responses . Their ability to induce defense responses provides us with a highly attractive alternative to conventional pesticides, if proven to be less toxic.This toxicity often leads to off-target effects against other organisms and the environment. As a result, the dangers of pesticide poisoning become more of a concern, making the identification of compounds that are not toxic, but instead stimulate plant’s inherent defenses very appealing. In addition to their potential use as pesticide replacements, synthetic elicitors can also be utilized as highly specific stimuli to perform more refined functional analyses of the plant defense network by interference with distinct network nodes. Their use should allow for the selective activation of certain regulatory circuits within this network. The identification of cellular targets of synthetic elicitors can uncover novel components of the plant immune system. Taken together the use of synthetic elicitors is likely to enable us to gain a deeper and more comprehensive understanding of the structure and function of the plant defense network. This report highlights the functional characterization of some members of the ACID cluster, a group of genes identified by micro-array experiments after treatment with two synthetic elicitors, DCA and INA . These 137 genes were found to be enriched for protein kinases, which may play key roles in plant defense signaling. Of the 16 ACID genes examined, ten were required for full basal defense of Arabidopsis against Hpa. Seven of the ten ACID genes have not been implicated as components of the plant immune system yet. While important for basal defense, these genes were not essential for immunity mediated by two distinct R-genes. Although they are transcriptionally activated by DCA, DCA mediated immunity was not compromised in their mutants. In addition, eight novel synthetic elicitors identified in the screen performed by Knoth et al., were further characterized. Notably, a synthetic elicitor was identified with a substantially lower active concentration than DCA. It was noted that DCA-mediated immunity in the acid mutants did not display the same hypersusceptibility seen in basal defense assays .

miRNAs are post transcriptional regulators that cause down regulation of target genes. Therefore, if a target gene is down-regulated by a miRNA, a negative correlation between miRNA expression and the target mRNA expression is expected. No statistically significant differentially expressed miRNAs were observed in our fruit small RNA seq data, so we instead predicted miRNAs that are potentially targeting DEGs found in fruit tissues. This approach was taken due to the complex regulatory networks that are known to exist in plants and other higher organisms. One miRNA may regulate many genes as its targets, while one gene may be targeted by many miRNAs. Both of these scenarios were observed in citrus roots in response to dehydration and salt stress. To evaluate these potential relationships in this study, the psRNA Target program was utilized, which accepts a list of known plant miRNAs in citrus and the coding sequence of the DEGs reported here to predict miRNAs according to the criteria described by Meyers et al.. Over 15,000 miRNA-mRNA interactions were predicted using psRNA Target. The RNAseq data was then utilized with an in-house R-script in order to select potential interacting pairs with an expected negative correlation in gene expression. After removal of genes that did not have any functional annotation, there were 366 combinations of miRNA-mRNA pairs that showed reciprocal expression patterns. Comparing these genes with the enriched GO terms and KEGG pathways led to several candidate miRNA-mRNA interactions that could be causing changes in fruit traits when differentially expressed between root stocks.

These genes included transcriptional regulators, hormone signal transduction genes, transporters,nft growing system and sugar metabolism genes. Based on the interacting pairs predicted and their relevance to fruit quality, 10 pairs of miRNAs and target mRNAs were selected for validation via qRT-PCR analysis . Samples collected at time points two and three were chosen for validation due to the larger differences in expression levels of genes in fruit grown on trifoliate orange compared to rough lemon root stocks at those times. For qRT-PCR, two biological replicates and three technical replicates were analyzed to quantify expression of each gene. Three miRNAs were up-regulated at both time points, while their target genes were down-regulated, two miRNAs were down-regulated at both time points, while their target genes were up-regulated, and the remaining five miRNAs validated were down-regulated at one time point and up-regulated at the other . The correlation between the relative expression level detected by qRT-PCR and by RNA-sequencing was calculated. Pearson correlation values were highly significant with r = 0.94, which strongly supported the sequencing data . However, certain miRNA-mRNA pairs did not have the expected fold changes from one time point to the next. For example, Csi-miR171a shows an increased fold change from September to November. This should correlate with a decreased fold change from September to November in the target gene , but instead, we see an increase in the target mRNA expression from September to November. Only this pair and Csi-miR1863 – ATEXP1 show this inconsistency. The results for the remaining eight pairs were consistent with their expected expression levels.

Figure 1.12 shows that seven of the miRNAs had increased expression levels in November compared with September, while three miRNAs decreased in expression from the during fruit development. The objective of this study was to correlate changes in gene expression of grafted citrus trees to effects in fruit quality due to varying root stocks. In this study, four root stocks were chosen from a root stock trial with Washington navel orange scion in Riverside, CA to assess for various fruit quality traits; Argentina sweet orange, Schaub rough lemon, Carrizo citrange, and Rich 16-6 trifoliate orange. Fruit quality data was collected from fruit grown on each of the four root stocks at the end of the growing season when fruit were ripe. In the present study, weight, height, width, rind color, rind texture, peel thickness, internal texture, juice weight, percent juice, total soluble solid and titratable acid levels were measured. The total yield and average fruit weights were markedly higher in navel orange fruit from trees grafted onto rough lemon compared to sweet orange, Carrizo citrange, or trifoliate orange root stocks. The rind thickness was also greatest on rough lemon root stocks compared with the other root stock-scion combinations. The most substantial differences could be seen in total soluble solids and acid levels. The highest levels of sugars and acids were found in fruit grown on Carrizo citrange. Trifoliate orange and sweet orange root stocks produced fruit with only slightly lower sugar and acid levels, while rough lemon produced fruit with significantly lower levels . This is consistent with the previously mentioned reports of root stock effects on fruit quality3,7-14. Presently, there is very little understanding of how root stocks influence citrus fruit quality, especially at the level of gene regulation. In this study, an integrated mRNA and miRNA high throughput sequencing analysis in fruit grafted onto genetically diverse root stocks was performed to help resolve potential mechanisms of root stock-scion effects on fruit quality. In the present study, RNA-seq was used to investigate transcriptome differences in the fruit of ‘Washington’ navel sweet orange grafted onto different root stocks and explore genes that may influence fruit quality traits. Juice vesicles from fruit grafted onto four genetically diverse root stocks at four different fruit development periods were sequenced. The RNA-seq approach detected a similar number of genes in all samples .

A large number of these genes were identified as differentially expressed over the course of fruit development, which is consistent with previous studies of transcriptome changes during fruit ripening in sweet orange . However, most genes showed similar temporal expression patterns among all root stock genotypes. Furthermore, only ~15% of the genes were genotype-specific . Therefore, the remainder of this study focused on DEGs identified between these root stock genotypes during fruit development.The majority of the differentially expressed genes are observed in comparisons involving rough lemon root stocks, especially compared to trifoliate orange. This is consistent with the observed differences in fruit quality traits, as fruit of trees grafted on rough lemon root stock showed consistent significant differences from fruit of trees grafted on the other three root stocks in many of the traits measured . These results suggest that rough lemon and trifoliate root stocks show the greatest effects on the scion and are good candidates to identify graft-related genes playing a role in fruit quality. The largest and most significant changes in gene expression between root stocks were observed at time points two and three . Among the DEGs were several genes with functions involved in fruit quality traits, such as those relating to starch and sucrose metabolism, fructose metabolism,nft hydroponic system and hormone signaling related genes. KEGG pathway analysis displayed plant hormone signal transduction, carotenoid biosynthesis, and fructose and mannose metabolism pathways to be significantly enriched. Several genes involved in various hormone-signaling pathways were DE, mainly genes in the abscisic acid and auxin-response pathways. Several genes involved in these pathways were chosen to validate the RNA-seq data by qRT-PCR due to their potential biological significance regarding root stock effects on fruit quality. ABA has been known to be a regulator of fruit ripening and response to abiotic stress in non-climacteric fruit. AHG1, a homolog of Arabidopsis PP2C family protein, was DE in this study. This gene was slightly up-regulated when comparing fruit of trees grafted on trifoliate to fruit of trees grafted on rough lemon root stock at time two and significantly down-regulated at time three . Upregulation of AHG1 is in accordance with previous studies showing this gene being induced by water stress, which may have occurred in September.

The down regulation of this gene later in the season could be correlated with increased fruit maturation in fruit grown on trifoliate root stocks. This is in agreement with a study in tomato where suppression of PP2C expression led to increased ABA accumulation and higher levels of ABA-signaling genes that increase the expression of ABA-mediated ripening-related genes. Auxin signal transduction is mediated by Aux/IAA and ARF genes. Aux/IAA proteins are negative regulators of the auxin signal transduction pathway. In this study, a gene encoding an Aux/IAA protein, IAA16, was up-regulated in fruit grown on trifoliate compared to rough lemon root stocks at time two and three . A previous study revealed that a gain-of-function mutation in IAA16 displayed reduced response to auxin and ABA, which led to reduced plant growth89. Silencing of related Aux/IAA genes increased fruit size in tomato due to auxin control of cell expansion and elongation. In addition to Aux/IAA, another early auxin-response gene, SAUR78, was DE in this study. This gene was down-regulated in fruit grown on trees grafted onto trifoliate compared to rough lemon root stocks at time two and three . Small Auxin Up RNA genes are a group of auxin-inducible proteins. SAUR78 over expression lines in Arabidopsis increased plant growth through interaction with ethylene receptor. Other SAUR genes have also been shown to promote cell expansion. Furthermore, a MYB77 gene encoding a transcription factor was DE in this study, displaying a slight increase in expression in fruit grown on trifoliate root stock at time two, but a large decrease in expression at time three . This gene was previously described as a regulator of the auxin signal transduction pathway. This protein was shown to interact with ARFs to promote plant growth. Interestingly, the effects of MYB77 in Arabidopsis were found to be increased by endogenous exposure to ABA and further promote plant growth. While these two studies were performed in roots, this transcription factor was shown to be involved in citrus fruit ripening, where it was highly correlated with ABA and suggested to have a similar function in response to the hormone28 . Although there were not statistically significantly differences seen in other genes in the auxin- and ABA-signaling pathways, trends could be observed during hierarchical clustering of these genes. Many of the genes within a family shared common expression levels and generally follow the predicted regulatory patterns in their respective pathways . Taken together, the changes in ABA- and auxin responsive genes suggest a potential mechanism for induced ripening by trifoliate root stock and larger fruit produced when rough lemon is used as a root stock. The expansion phase of citrus fruit development involves cell enlargement and water accumulation. Given the changes in hormone-signaling pathways that likely lead to changes in fruit size, other genes related to fruit growth, such as transporters and genes related to cell wall metabolism were investigated. This led to the identification of two DEGs that could be influencing fruit size. The first, a Plasma membrane Intrinsic Protein 2gene encoding an aquaporin was down-regulated in fruit grown on trifoliate root stock . Water import in plants is mediated by aquaporins and essential for cell expansion. These genes were highly expressed in expanding green grapes and one was identified as a candidate gene under the QTL for berry weight. PIP genes were also associated with an increase in volume of fruit in apple and strawberry. The second DEG, an expansin , was also down-regulated in fruit grown on trifoliate root stock . Expansins play various roles in fruit development, including cell elongation and cell wall softening. A homolog of EXP1 in tomato was expressed during green fruit cell division and expansion with maximum accumulation of EXP1 during the late phase of green fruit expansion and early maturation. The increase in expression of these two genes in fruit grown on rough lemon root stock could contribute to the larger fruit size observed. In addition to cell division and cell expansion, during fruit development, fruit softening is also an important feature that relies on cell wall metabolism. The Trichome Birefringence-Likegene, which encodes a protein required for cellulose biosynthesis, was identified in our study as DE. Mutations in this gene caused a reduction in the amount of pectins and an increase in pectin methylesterase activity. PME catalyses the demethylesterification of pectin, which may undergo depolymerisation by glycosidases. TBL23 was up-regulated in fruit grown on trifoliate root stock compared to rough lemon , suggesting a potential role in fruit softening during citrus ripening. Transcription factors also play an important role in plant development and fruit ripening.

Several of these chromosomes also showed significant associations with this study, but the verified region on 4B was not among them. Similar to our results, individual QTL were almost always exclusive to each population. Kabir et al. identified QTLs for root number on 1B, 2A, 3A, 4A, 4D, and 7A and no QTL was consistent across the two populations. These observations suggest two explanations: either seminal root number is sensitive to environmental effects and many statistically significant associations detected in all studies are spurious, or this trait is controlled by a large number of genes, in different combinations in each parental line. No single locus appears to have a large dominant effect, perhaps with the exceptions of the loci on chromosomes 2DS and 4BL in our study. Unfortunately the two studies of Zhang et al and Kabir et al did not investigate seminal root angle so we have no insight into how that trait behaved in both cases. Within our populations, the expression of seminal root angle QTLs were also highly dependent upon year and population, however, five QTLs were consistent across both years . One of those QTL, QRA.ucr-2D, rolling bench was also verified within two of the three populations . This QTL accounted for the largest proportion of the phenotypic variation of all verified QTLs. This could potentially be due to the greater phenotypic difference between the two parents in the SC and SF populations which allow for greater detection of QTL .

Using relative genetic map distances this QTL appears to be the same QTL as identified by Bektas with a large effect upon other root traits such as deep root weight. Bai et al. also reported a QTL on chromosome 2D for seminal root biomass. In other cases such as QRA.ucr-6A and QRA.ucr-7B the QTLs consistently appeared in the SC population in both years; however, they do not appear in other populations. Given the crossing pattern used in the development of the populations, and even with an assumption that the QTL donor carries the same allele as Foisy, segregation should have been observed in the CF population, but it was not. Perhaps this is because this QTL explains a small percentage of the total phenotypic variation and its effect is overshadowed, hence undetectable, by segregation of different allelic combinations within the SF population. In the CF population qRA.ucr-5B and qRA.ucr-7A varied more from one year to the next than any other QTL, and no association with common markers were detected, even though on the consensus map of Wang et al. all these associated markers fall within 10-20cM of one another. Because the effect of this specific genome region was reproducible it is deserving of further study. These shifts of QTL positions are often associated with changes in the total amount of variation explained by the QTL between years. For example, qRA.ucr-5B in the CF population explained 9.40 % of the phenotypic variation in 2014 but 19.50% in 2015. These QTL appear verified as they produce significant effects in both years, however, their effects were not detected in the other two populations.

This may be an effect of considerable plasticity of the characters measured, illustrating technical difficulties in precise phenotyping. On the other hand, this may hint at the existence of closely linked loci within the same family, each with a minor effect on the total expression of the character, and minor variation within the environment from one year to the next may cause shifts in the locus/loci responsible, thus changing marker associations in the region. These examples could potentially be shedding light on the plasticity of QTL for seminal root angle in light of environmental cues. New techniques such as the clear pot method proposed by Richard et al. may provide less variability by reducing the experimental error. Unraveling the genetics of seminal root angle in wheat may prove to be a longer road than in other crops like rice. Uga et al. identified DEEPER ROOTING 1as a gene controlling the gravitropic response of roots and thus the angle of root growth. Higher expression of DRO1 caused roots to grow more downward and when introduced into a shallow rooted cultivar it improved grain yield under drought by enabling access to water deeper in the soil profile. It is likely simpler to study quantitative traits like seminal root angle within the smaller diploid genome of rice. Although there is synteny between rice and wheat within the region where DRO1 was identified, QTL in that region were not identified. Until recently rice was the closest relative of wheat that had information about seminal root angle genetics. However, researchers interested in barley have now begun to study seminal root traits as well . Using the clear pot method demonstrated by Richard et al. they were able to identify seven QTLs for seminal root angle and number . Using cross species analysis they were able to identify 10 common genes underlying root trait QTLs in barley, wheat, and sorghum.

Perhaps as seminal root angle is unraveled in barley, a closer relative to wheat than rice, it will provide insights which may aid in our understanding of wheat seminal root trait genetics. Seminal root angle and number appear to be interrelated and both appear to be related to seed weight . In the SC population root number and angle are negatively correlated so that seeds with more seminal roots have narrower angles and vice versa. This correlation explained 22% and 30% of the variation seen in 2014 and 2015 respectively. In the SF population seminal root number and seed weight were positively correlated so that heavier seeds tended towards a higher number of seminal roots. That correlation explained 36% and 45% of the variation in 2014 and 2015 respectively. In the CF population all these characters are correlated where seminal root number is positively correlated with seed weight and seminal root angle is negatively correlated with number and weight. The correlation between root number and seed weight explained 46% of the variation in 2014 and 2015, seminal root number and angle explained 24% and 33% in 2014 and 2015 respectively,grow table hydroponic and the correlation of seminal root angle and seed weight explained 23% and 35% of the variation. These results show that in the CF population a significant amount of the variation can be explained by these interactions. This is interesting in that those two parents have more similar seminal root angles . Since seed weight explained a significant amount of the variation for root number and angle it could mean loci for seminal root angle or number in CF are actually seed weight QTLs. The only way to ascertain which character is actually monitored is to map QTLs for seed weight and test their associations with those found for seminal root angle and number. In the SC and SF population no QTL for seed weight was similar to that mapped for root angle and number. However, in the CF population two QTLs for seed weight were in similar positions to QTLs for root angle and number . The QTL for seed weight on chromosome 1B clearly overlaps with the QTL for root number on 1B, each sharing common markers in both years. Of the QTLs mapped for root number in CF this QTL on 1B was the only one observed in both years. For the QTL on 5B there are not any overlapping markers for the root angle QTL and seed weight QTL, however, the QTLs for root angle on 5B shift from one year to the next making this region suspect and deserving of further inquiry. Of the QTLs for root angle in the CF population the QTL on 5B explained the greater portion of variation seen in the population over two years. Since so much variation is explained by the interaction of seed weight with angle and number it is not a major leap to assume this region could be associated with seed weight and inadvertently associated with root angle. Given those results, coupled with the correlation analysis, it seems that seed weight is a major factor, if not the major factor, in the CF population giving rise to most differences in seminal root traits. These interactions between seed weight, seminal root angle and seminal root number indicate the high complexity of root traits.

The nature of these interactions has not been tested but it appears plausible that when five seminal roots are initiated they occupy greater space at the developing point of the embryo than when only three roots are initiated. This may force the inner pair of roots more downward, thus reducing the angle between them and explain why more seminal roots is correlated with narrower angles of growth and why those with less seminal roots have a tendency toward wider angles. Additionally, heavier seeds are correlated with higher seminal root numbers which then may influence the association of seed weight with seminal root angle. Perhaps this argument is overly simplistic, and it does not begin to explain why these three characters are correlated only in some populations, and why the levels of interaction change from one population to the next. Another explanation could be linkage of loci for individual traits which could make them difficult to tease apart. In any case, these correlations underscore the complexity of these traits and call for further dissection of each trait and their interactions, so that actual genetic effects are studied. Those interactions could lend new dimensions of complexity when considering the inheritance of seminal root angle and number. These findings also provide new information for considerations when designing future projects centered on these traits. Another point to be made is that QTLs in other studies should be further verified and looked at again through this perspective. As far as we know, other studies did not map QTLs for seed weight when an interaction was observed with seminal root traits. Since the green revolution, semi-dwarf high yielding wheat cultivars have become a standard in commercial production. The semi-dwarf character of wheat lead to a threefold increase in grain yield and provided food security for developing countries . These green revolution wheats were selected for under high-input farming practices which led to a decrease in root biomass . A greater understanding of root traits and how those traits relate to whole plant strategies may enable breeders to increase yields under drought conditions . This understanding can only come by actively studying the root system in a controlled environment and until the relationship of root and shoot traits is better understood we cannot determine how to improve a plants ability to be productive in a fluctuating environment. Roots absorb water and nutrients while also anchoring the plant to the soil. The shoots utilize those resources for photosynthesis and are the site of sexual reproduction. All these functions must work together in coordination for the plant to thrive within its environment. In general plants maintain a fairly strict harmony between shoot and root biomass partitioning . However, during different growth and developmental stages the partitioning of biomass does fluctuate. In the early stages of growth resource allocation and biomass accumulation is focused towards the roots but that shifts considerably as the plant reaches flowering with the major part of photosynthates directed to the shoots . These general principles were supported by Frageria who demonstrated that the root-to-shoot ratio in wheat, as well as other crops, decreased as plants advanced in age. For these reasons it is essential to understand what effect any changes to these general principals may have upon yield within wheat and other crops as well. Increased root biomass increases grain yield under limited or rain-fed environments . This is likely due to the ability of a larger root system to absorb water and nitrogen from the soil; an added benefit is reduced leaching and agricultural run-off . What remains unclear is if increasing root biomass will continue to increase grain yields. This issue has been touched upon in wheat by Maheepala et al. leaving plenty of room for further inquiry and testing.

Other related taxa include uncultured clones from a variety of engineered and natural environments, including: wastewater digesters in France and the United States, estuarine sediments in Taiwan, peat wetlands in Japan, sinkholes in Mexico, and hydrothermal vents in the Pacific Ocean . Whether or not the capacity for DPO is a common feature of this clade remains to be seen, as there is evidence of lateral acquisition of phosphite oxidation genes in FiPS-3 as well as in several APO-capable bacteria . Indeed, whether Phox-21 itself is capable of growth by DPO coupled to CO2 reduction in pure culture has yet to be confirmed, since efforts to isolate this organism have so far proven unsuccessful.The work presented in Chapter 3 revealed the presence in my wastewater enrichments of a novel bacterium from an uncultured clade within the Deltaproteobacteria whose abundance was strongly correlated with DPO activity. Based on this evidence, I hypothesized that this bacterium, designated as strain Phox-21, was the organism responsible for phosphite oxidation in my cultures. However, as my attempts to isolate Phox-21 were unsuccessful, I was unable to confirm that it was capable of carrying out this metabolism in pure culture. Therefore, I decided to perform a metagenomic analysis of some of the DNA samples I had previously collected for 16S rRNA gene analysis in order to look for possible functional markers of DPO, such as the ptx-ptd genes,grow hydroponic in the genome of Phox-21. In addition to establishing a more conclusive link between Phox-21 and DPO, I also hoped that genomic profiling of this organism would reveal its broader metabolic characteristics and provide insights that could aid in its isolation and culturing.

Furthermore, I expected the metagenomic dataset to shed light on the metabolic capabilities of other enrichment community members, thus providing a wider ecological context for the role of DPO in this system.Coates Genomics Sequencing Laboratory at UC Berkeley for sequencing on an Ilumina HiSeq 2000 . Ilumina sequencing reads were trimmed for quality and filtered using Sickle v1.33 with a quality threshold value of 28 and good-quality paired-end reads were then merged using IDBA-UD v1.0 . Merged reads from all samples were combined and assembled using MEGAHIT v1.0.2 with default parameters . MEGAHIT is an assembler developed specifically for metagenomic reads that uses succinct de Bruijn graphs and an iterative multiple k-mer size strategy. Merged reads from each sample where then mapped backed to the combined assembly using BWA-MEM v0.7.10 with default parameters in order to assess sequencing coverage . Contigs from the combined assembly were binned into individual genomes using the Anvi’o v1.1.0 platform . Anvi’o generates hierarchical clusters of related contigs using both tetranucleotide frequency and coverage across samples as the clustering parameters. The platform also provides a visualization interface that allows the user to further refine the contig clusters into genome bins based on coverage, GC content, and phylogenetic marker genes. Furthermore, Anvi’o assigns taxonomic lineages to the genome bins based on the presence of phylogenetic marker genes. Genome bins generated with Anvi’o were subsequently assessed for completeness and contamination based on the presence of lineagespecific, conserved, single-copy marker genes using the automated bin evaluation tool CheckM v1.0.1 . CheckM calculates ‘completeness’ based on the number of expected marker genes that are present in a given bin and ‘contamination’ based on the number of marker genes that are present in multiple copies and have less than 90% amino acid identity to each other.

High-quality genomes were submitted to the Integrated Microbial Genomes database for gene calling and annotation . IMG utilizes Prodigal v2.50 for identification of protein-coding genes, which are then functionally annotated using a custom, manually-curated pipeline based on BLAST and HMMER searches against multiple protein databases .The presence of a ptx-ptd gene cluster in the genome of Phox-21, as well as its higher abundance during phosphite-oxidizing conditions, clearly indicates that this is the organism responsible for DPO in our enrichments. In addition, the observed CO2 dependence of DPO in our enrichments coupled with the fact that no other terminal electron acceptors were added to our media implies that Phox-21 is capable of growing by coupling phosphite oxidation to CO2 reduction. The presence of a formate dehydrogenase complex FdhAB similar to that of M. thermoacetica in Phox-21 provides a putative means by which CO2 reduction could occur. However, the absence of key WLP genes suggests that this organism is unable to generate acetyl-CoA from CO2 alone and therefore is not a true autotroph. Furthermore, it lacks an electron transport chain and thus appears to be incapable of energy conservation through oxidative phosphorylation. Instead, we propose that Phox-21 couples phosphite oxidation to CO2 reduction to formate by means of FdhAB and uses the energy generated by this reaction to assimilate organic carbon sources such as acetate . Based on thermodynamic calculations and physiological evidence, Schink et al. have previously proposed that FiPS-3 is able to conserve energy during DPO by directly generating ATP as well as NADH from the oxidation of phosphite. This putative substrate-level phosphorylation step during DPO is likely mediated by PtdFHI and would allow for energy conservation in the absence of membrane-associated electron transport .

ATP produced in this manner could be used by Phox-21 to incorporate acetate into biomass via AcsM and the partial TCA cycle as well as to run the proton and sodium translocating ATP synthases in reverse in order to establish an ion motive force across the cell membrane . The resulting sodium ion gradient could drive the RNF complex to reduce ferredoxin, which could then serve as an electron donor for pyruvate synthesis by the PFOR enzyme as well as for NADPH production by the NfnAB complex . The FocA transporter could serve both to import acetate for assimilation and to export formate from the cell as a metabolic waste product . However,mobile grow system in the presence of nitrite, formate could be re-oxidized to CO2 by FdoGHI coupled to the reduction of nitrite by NrfAH . This reaction would contribute to the maintenance of a proton motive force and would also yield ammonia, which could be imported into the cell via the AmtB transporter to serve as a nitrogen source. Our metabolic model predicts that Phox-21 should require an organic carbon substrate such as acetate for growth and should also excrete formate into the medium as a product of CO2 reduction. A requirement for organic carbon may at least partly explain the stimulatory effect of rumen fluid on DPO, since rumen fluid has been shown to contain as much as 60 mM acetate in addition to various carbohydrates, organic acids, amino acids, and fatty acids . Additionally, Phox-21 is predicted to be incapable of synthesizing alanine, histidine, threonine, or THF, all of which were absent from our original growth media but may be present in rumen fluid. However, attempts to grow our enrichments in media supplemented with acetate, THF, and amino acids but lacking rumen fluid have so far resulted in substantially lower phosphite oxidation rates, indicating that there may be other components in the rumen fluid that promote the growth of Phox-21. Acetate present in rumen fluid amended cultures could also have served as a growth substrate for the Tepidanaerobacter strains and methanogens present in the communities.

Both Tepidanaerobacter genomes have all the genes for the carbonyl branch of the WLP but lack a formate dehydrogenase and an uptake hydrogenase, which is consistent with previous genomic analysis of Tepidanaerobacter acetatoxydans and indicates that these organisms are capable of syntrophic acetate oxidation but not of autotrophic growth . Likewise, both Methanoculleus sp. EBM-46 and Methanococcoides sp. EBM-47 appear to be capable of acetoclastic methanogenesis, although only EBM-46 has the genes necessary for growth on H2/CO2 and formate as well. The remaining enrichment community members had no WLP genes and mostly lacked genes involved in respiratory processes and were therefore likely involved in the fermentation of organic acids, amino acids, and carbohydrates present in the rumen fluid. DPO was discovered over a decade ago in the marine sediment isolate D. phosphitoxidans FiPS-3, but there had so far been no additional reports of this metabolism in other environments. This study, therefore, represents only the second ever observation of DPO and the first ever description of a community structure and metagenome related to this metabolism. Furthermore, the organism responsible for phosphite oxidation in our system, Phox-21, is a novel bacterium belonging to a candidate order within the Deltaproteobacteria that currently has no cultured representatives. Although my attempts to isolate Phox-21 were unsuccessful, metagenomic analysis revealed the presence of a ptx-ptd cluster in its genome, similar to the one found in FiPS-3. Previous work has shown that ptxD and ptdC are necessary for phosphite oxidation in FiPS-3 . Additionally, as part of this study, I found that ptdFGHI are significantly upregulated in FiPS-3 in the presence of phosphite. That ptdCFHI are also found in Phox-21, but not in any other genome currently available in the IMG database, is further evidence that these genes play an important role in DPO. Interestingly, ptdG is present in FiPS-3 but not in Phox-21, which suggests that this gene may not be essential for DPO in every organism, although it may still be required by FiPS-3. However, much work is still needed in order to elucidate how energy for growth is conserved during DPO. The involvement of PtdFHI in this process has yet to be experimentally confirmed and the mechanism of action of these enzymes has not been determined. Whether ATP is indeed produced from substrate-level phosphorylation during DPO is another outstanding question that requires additional experiments, both in vivo and in vitro, in order to conclusively address. It is assumed to function as a phosphite/phosphate antiporter based on its homology to known antiporters, but this assertion still needs to be tested. The presence of an incomplete Wood-Ljungdahl Pathway in Phox-21 was unexpected, since we had previously assumed that it was capable of growing autotrophically. Nonetheless, this predicted requirement for organic carbon could at least partially explain why the growth of Phox-21 improved so markedly when rumen fluid was added to the enrichments. Although there have been previous reports of organisms with incomplete WLPs , to our knowledge, this study provides the first genomic evidence of an organism capable of using CO2 as a terminal electron acceptor but not as a carbon source. Due to its extremely low redox potential, phosphite is the only known biological electron donor that could drive the reduction of CO2 to formate while generating enough energy to produce ATP for the incorporation of acetate into biomass. As such, this unprecedented metabolism may be unique to DPO-capable organisms. However, as discussed above, the feasibility of this proposed metabolism hinges on whether or not DPO can generate ATP through substrate-level phosphorylation, which is still an open question. Still, the apparent lack of any electron transport chain components in Phox-21 suggests that under phosphite-oxidizing, CO2-reducing conditions, energy conservation in this organism would have to proceed exclusively by means of substrate-level phosphorylation. Ultimately, though, this metabolic model still needs to be experimentally confirmed. I have so far been unable to detect significant formate production or acetate consumption under DPO conditions in my enrichments. However, it may not be possible to detect these processes in enrichment cultures due to the presence of other community members capable of using formate and producing acetate. Obtaining a pure culture of Phox-21 would therefore greatly facilitate any future investigations of its physiology. The environmental prevalence and phylogenetic diversity of DPO-capable organisms remains unclear. Like FiPS-3, Phox-21 belongs to the Deltaproteobacteria, but the sample size of known DPO-capable organisms is still far too small to allow us to determine whether this metabolism is restricted to a specific phylogenetic group. There is evidence that the ptx-ptd genes in FiPS-3 were acquired by lateral gene transfer, but we do not know how common it is for these genes to be horizontally propagated in the environment or what the phylogenetic range of these events might be.