Microbial mats have played an important role in the carbon (C) and nutrient cycles since the Archean Eon and modern mats are important contributors to the biogeochemistry of intertidal wetlands. Microbial mats are flat assemblages of microbes that are currently found in many unvegetated habitats globally. Intertidal salt pans are a common habitat for microbial mats, however little is known about the distribution of microbial mats within the intertidal landscape. Understanding the spatial distribution of microbial mats is critical to developing quantitative estimates of the impacts of microbial mats on their ecosystems. We photographically measured the presence and density of microbial mats within 1 m2 quadrats across a landscape scale (~1000 Ha) on the Gulf Coast of Florida. The wide variety of metabolic processes that are found within microbial mats makes the net biogeochemical impacts of the microbial mats highly variable as well. To explore the biogeochemistry associated with microbial mats, we measured a suite of soil attributes under microbial mats and compared those measurements to nearby soils without microbial mats. We found that microbial mats are found on soils with biogeochemical attributes that are significantly different than soils without microbial mats. Soil organic matter, nitrate concentration, and soil temperature significantly increased in soils under microbial mats; pH was significantly lower in soils under microbial mats. Also notable was although the concentration of soil organic matter was higher, the bioavailability of that organic matter was significantly lower. Microbial mat presence is correlated with geomorphic variables such as proximal boundaries, as well as neighboring vegetation and other microbial mats.

Thesis advisor: Gail C. Kineke / An observational study was conducted from 2013 to 2016 to investigate suspended-sediment transport processes in the stratified Connecticut River estuary. Time-series measurements of velocity and suspended-sediment concentration from the upper estuary were analyzed to determine the relative importance of different processes driving sediment flux under highly-variable river discharge. Results indicate that under high discharge the salt intrusion is forced towards the mouth causing large seaward sediment fluxes throughout the water column. Seaward fluxes are dominated by mean advection, with some contribution due to tidal pumping. Under low discharge the salt intrusion extends to the upper estuary, advancing as a bottom salinity front during each flood tide. Stratification and strong velocity shear during the ebb tide cause the upper and lower water column to become dynamically decoupled. Sediment flux near the bed is landward throughout the tidal cycle despite the net seaward depth-integrated flux, and is almost fully attributed to the mean estuarine circulation. River discharge is the primary factor affecting the magnitude and direction of sediment flux because of its high variability and direct connection to the salt-wedge dynamics. A generalized three-phase conceptual model describes suspended-sediment transport in shallow, stratified estuaries with low trapping efficiencies. First, fine sediment bypasses the estuary during high river flows and exports to the coastal ocean where a portion of this sediment is temporarily deposited outside the mouth. Second, during low discharge offshore mud deposits are reworked by wave- and tidally-driven currents and some sediment is advected back into the estuary with the advancing salt intrusion that transports sediment landward. Third, spatial salinity gradients facilitate sediment transport from the main channel to channel margins, marshes and off-river coves where it is retained and deposited long-term, as demonstrated in prior studies. This re-introduction and trapping of recycled sediment under low-discharge conditions can have important implications for pollutant transport, shoaling of navigation channels and harbors, and salt marsh accretion in the face of rising sea levels. / Thesis (MS) — Boston College, 2018. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Earth and Environmental Sciences.

Phospholipid molecules self-assemble to form bilayers that are poorly soluble in an aqueous solvent. Phospholipids may, however, be readily dissolved by mixing with a bile salt or amphiphilic drug surfactant that forms mixed surfactant/phospholipid micelles. Mixed bile salt/phospholipid micelles play an important role in the digestion of fats in the gastrointestinal tract as well as solubilizers of water-insoluble drugs and other drug delivery applications. The ability of surfactants to dissolve phospholipids largely depends on the chemical structure of both surfactant and phospholipid. While bile salt and amphiphilic drug surfactants, with a rigid chemical structure, are good solubilizers of phospholipids, conventional surfactants, with a flexible aliphatic hydrocarbon tail, are poor solubilizers. In addition, the chemical structure of phospholipids, such as tail lengths and charge number, or the fraction of a cosurfactant, for instance cholesterol, is expected to influence the ability to form mixed micelles. In this paper, the aggregation behaviour and mixed micelle formation of the phospholipid dimyristoyl phosphatidylglycerol (DMPC) and two different surfactants: the anionic surfactant sodium dodecyl sulfate (SDS) and the amphiphilic drug surfactant Sodium fusidate (SF, similar structure to that of bile salt), have been studied, and the transition from micelles to bilayers has  been determined for the different surfactants, as well as the size and structure of micelles and bilayers close to the points of transition. The self-assembly of the mixed micelles of surfactants/phospholipids have been investigated using surface tension measurements, refractive index increment and static and dynamic light scattering (SLS and DLS). The results suggest that the transition from micelles to bilayers are found to exist in the following range of bile salt/phospholipid compositions: For SF, 70-75 mol % phospholipid in the micelle was determined to be the point of transition, whilst 20-30 mol % for SDS. As the mole fractions of DMPC increased for both mixtures, the samples became turbid, which indicates the transition of micelles to bilayers. An exact value for molar ratio of transition might not be possible to determine from this study, but instead a, somewhat wider, range of values. In spite of this, a clear trend and difference between the two surfactants was observed.

>Magister Scientiae - MSc / In agriculture crop productivity is greatly affected by stresses such as salinity, drought, temperature and honnonal changes of crop plants and responses to these stresses. Studies have shown that a natriuretic peptide based regulatory system responsible for water and ion homeostasis in animals has a hctcrologous equivalent in plants. Plant natriuretic peptide immunoreactants (irPNPs) have been reported to be involved in K+, Na+ and er ions fluxes in plants. Previously, an Arabidopsis thaliana transcript (AtPNP-A) encoding an irPNP (AtPNP-A) has been identified and isolated (Ludidi et al., 2002). The AtPNP-A a novel protein and part of its physiological role is presented here.

Food security is a major concern of the 21st century, given climate change and population growth. In addition, high salt concentrations in soils affect ~20% of irrigated land and cause a substantial reduction in crop yield. Cultivating salt-tolerant crops could enable the use of salt-affected agricultural land, reduce the use of fresh water and alleviate yield losses. Innovative methods need to be developed to study traditional and novel traits that contribute to salinity tolerance and accurately quantify them. These studies would eventually serve for developing new salt tolerant crops, adapted to the harsh arid and semi-arid climate conditions. A study of 200 accessions of the wild tomatoes (Solanum pimpinellifolium) was conducted in field conditions with phenotyping using an unmanned aerial vehicle (UAV)-mounted hyperspectral camera. Six genotypes with different levels of salt tolerance were sampled for leaf pigment analyses, revealing a clear pattern for the high salt tolerant accession M007, where pigment content in the salt-treated plants significantly increased compared to their control counterparts only in harvesting campaigns 3 and 6, each performed two days after the first and second salt stress application events. Moreover, the light harvesting capacity was found to be better maintained under salt stress in the medium (M255) and highly salt tolerant (M007 and M061) accessions. Pigment quantitation data will contribute towards the groundtruthing of hyperspectral imaging for the development of remote sensing-based predictive pigment mapping methods. This work establishes a reliable quantification protocol for correlating pigment content with vegetation indices. Hence, pigment content captured by imaging techniques and validated using biochemical analysis would serve in developing a high-throughput method for pigment quantitation in the field using UAV-based hyperspectral imaging. This would serve as a tool for measuring pigment content in large number of genotypes in the field which would eventually lead to new salt-tolerant genes.

Barley is a resilient crop that performs better than other cereal plants under abiotic stress conditions, including salinity stress. The understanding of salinity tolerance in crops is a major milestone to increase yield in areas affected by soil salinity. In barley, some components of salinity tolerance have been elucidated, (e.g. HVP10, which is involved in tissue tolerance), yet little research has explored the discovery of other components contributing to salinity tolerance. In this PhD project, a forward genetics approach was used, whereby two barley populations were phenotyped under controlled and field conditions for salinity tolerance. The first population is a diversity panel of two-row European spring barley, and the second population is a nested association mapping barley population with wild donors from the Fertile Crescent. The use of non-destructive high-throughput experiments conducted under controlled conditions provided insight into the understudied shoot ion-independent component of salinity tolerance. In addition, the previously known association HvHKT1;5 was detected under controlled conditions. In parallel, the field experiments increased our understanding of new components of salinity tolerance, such as the maintenance of yield and yield-related traits under saline conditions. This strategy was successful with the identification of a locus on chromosome 2H (140-145 cM), where the allele from one of the wild donors of the nested association mapping population increased yield under saline conditions in the field. When re-evaluating lines homozygous at the 2H locus, ear length, ear number per plant, yield and harvest index were all significantly higher under saline conditions for the lines carrying the wild allele. Furthermore, another interesting locus on chromosome 7H that was responsive to salt treatment and co-localized with HVP1 was identified using the diversity panel population. Loci with known flowering genes were also shown to be involved in salinity tolerance. To conclude, this PhD project shed more light on the genetic mechanisms of salinity tolerance in barley, a knowledge that can benefit breeding programs and can be extended to other crops such as wheat.

For more than half of the world’s population, rice (Oryza sativa L.), the most saltsensitive cereal, is a dietary staple. Soil salinity is a major constraint to rice production worldwide. Thus, to feed 9 billion people by 2050, we need to increase rice production while facing the challenges of rapid global environmental changes. To meet some of these challenges, there is a vital requirement to significantly increase rice production in salinized land and improve photosynthetic efficiency. Exposure of plants to soil salinity rapidly reduces their growth and transpiration rates (TRs) due to the ‘osmotic component’ of salt stress (sensu Munns and Tester), which is hypothesized to be related to sensing and signaling mechanisms. Over time, toxic concentrations of Na+ and Cl− accumulate in the cells of the shoot, known as the ‘ionic component’ of salt stress, which causes premature leaf senescence. Both osmotic and ionic components of salinity stress are likely to impact yield. Despite significant advances in our understanding of the ionic components of salinity tolerance, little is known about the early responses of plants to salinity stress. In my PhD project, the aim was to analyze naturally occurring variation in salinity tolerance of rice and identify key genes related to higher salinity tolerance using high-throughput phenomics and field trials. I used a forward genetics approach, with two rice diversity panels (indica and aus) and recently published sequencing data (McCouch et al., 2017). Indica and aus were phenotyped under controlled conditions, while the indica diversity panel was also further studied under field conditions for salinity tolerance. I also examined previously unexplored traits associated with salinity tolerance, in particular the effects of salinity on transpiration and transpiration use efficiency. The non-destructive high-throughput experiments conducted under controlled conditions gave insights into the understudied shoot ion-independent component of salinity tolerance. In parallel, the field experiments increased our understanding of the genetic control of further components of salinity tolerance, including the maintenance of yield under saline conditions. Importantly, this project also aimed to improve the current association methods of GWAS by exploring and testing novel Mixed Linear Models. One major benefit of this Ph.D. project was the development of a more holistic approach that recognizes the complexity of the genotype–phenotype interaction. The purpose of my work was to shed more light on the genetic mechanisms of salinity tolerance in rice and discover genes associated with traits contributing to higher photosynthetic activity under both controlled and field conditions. This will ultimately lead to further exploration of the genetic diversity present in the PRAY indica panel, in order to develop higher yielding rice varieties.

I designed a suite of studies in coordination with Utah Division of Wildlife Resources (UDWR) to evaluate waterfowl use of the GSL in winter and ecological aspects associated with GSL use. These studies provided insight into key information gaps previously identified by UDWR regarding management of GSL resources. Population surveys indicated total duck abundance was low when GSL surface elevations were low and wetland resources diminished because of persistent drought in the system. Also, ducks appear to use hypersaline parts of GSL more when freshwater habitats are limited from either drought or ice conditions. Common goldeneye, northern shoveler, and green-winged teal exhibited the most use of hypersaline areas. Dietary evaluations indicated all three species feed on hypersaline invertebrates from GSL to meet energetic and nutritional needs in winter. Brine shrimp cysts were important foods for northern shoveler and green-winged teal. Fat levels of ducks are important determinants of survival and fitness. Fat reserves of goldeneye were generally lower in the winter when both GSL and wetland habitat resources were lower. Results suggest brine fly larvae productivity, freshwater habitat availability, and temperature and wind speed likely play a more prominent role in goldeneye fat reserves than osmoregulation. Also, common goldeneye and northern shoveler using the GSL apparently accumulated biologically concerning amounts of mercury and selenium during winter. However, further research is needed to evaluate the effect of these elements on GSL ducks.

A two-dimensional, finite-element, porous-media flow model is developed to simulate stratified bi-directional flow of brine through the earth embankment carrying the Southern Pacific Railroad across Great Salt Lake. The model is part of a two-year research program whose objective is to develop a computer model of circulation in Great Salt Lake. This overall model is to be used as a predictive device for salinity distributions and circulation patterns in the lake. The porous media flow model is designed to establish flow rates through the Southern Pacific Railroad causeway embankment which traverses the north central part of he lake and divides it into two bodies of water. The study first develops the mathematical equations which describe two-dimensional stratified bi-directional flow of a fluid through porous media. Next , the problem is numerically posed as a boundary value problem in terms of pressure. This formulation is then solved by an iterative finite element scheme which employs quadratic, isoparametric, quadrilateral elements. The study also investigates two possible means of performing an analysis of stratified bi-directional flow with a pressure formulation by either posing the problem as a single boundary value problem with two densities of fluid within, or as two single-density boundary value problems coupled at the density interface. The single boundary formulation did not converge with the techniques attempted due to numerical instability at the density interface. The numerical model developed enables one to calculate fluid flow rates as well as the locations of the free surface and density-interface. The model simulation investigates many lake variables which affect brine flows through the embankment. Realistic model parameters are used which cover the range of actual values observed on the lake for the years 1968 through 1972. The numerical results presented in the study are given in terms of generalized dimensionless variables. The numerical results appeared to be in agreement with previously performed stratified bi-directional Hele-Shaw model studies. The major lake parameters affecting flow rates through the causeway were the free surface head difference, the southside lake surface elevation and the difference in fluid densities between the upper and lower layers of the embankment . The southward density flow was found to be completely cut off for certain combinations of lake parameters. Lack of adequate field data collected on the embankment has left both the geometry and the coefficient of permeability of the fill in question, preventing a rigorous verification of the model' s ability to predict actual flows. More field data are also necessary to establish whether there is stratification on the north side of the embankment which can greatly affect flow calculations. A high Reynold's number was found for flow through the embankment, raising a question as to the validity of the Darcian flow assumption used in the analysis. However, the establishment of the true Reynold's number can only be verified through the collection of more empirical data.

Results of past studies on the spring-fed salt marshes of Utah indicated that waterfowl production on these areas was much lower than on Utah's river-fed marshes. Waterfowl production on the newly-established Fish Springs National Wildlife Refuge, a spring-fed marsh, increased considerably, however, after its waters were impounded. It was believed that by determining what caused this increased production at Fish Springs it would be possible to obtain greater waterfowl production a t other spring-fed marshes. Consequently waterfowl populations and factors affecting waterfowl production on this marsh were studied during the summers of 1966, 1967, and 1968. Populations of breeding ducks averaged approximately 900 pairs a year in 1967 and 1968. Mallards, cinnamon teal, and redheads comprised about 80 percent of these birds. Nesting densities, on plots representing available habitat, averaged about one nest per acre during these two years. In 1967 and 1968 a total of 312 duck nests representing 10 species were studied and their fates determined. Overall nest success was 63 percent, and predators, principally coyotes and striped skunks, destroyed 25 percent of all nests. Calculated duckling mortality rates during 1967 and 1968, respectively, were 19 and 16 percent. Duck production at Fish Springs averaged about 3,000 birds or about 430 ducks per square mile of marsh habitat a year during this period. At present the sparsity of adequate nesting cover for gadwalls appears to be an important limitation to breeding by this species at Fish Springs. Nesting cover apparently has not limited the use of this marsh by other waterfowl species, however, as evidenced by a high incidence (76 percent) of nesting on dry ground by redheads and ruddy ducks. Aquatic insect sampling in waters inundating portions of the original Fish Springs marsh indicated that these waters produced large quantities of proteinaceous foods for ducklings. Populations of aquatic insects in the original marsh were probably low except in recently disturbed areas. It appears that limitations of brood-rearing habitat were primarily responsible for low waterfowl production in the past. Newly-created impoundments, rich in animal food, were probably the key to the increase in waterfowl production on this marsh.