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Increasing cyanobacterial harmful algal blooms (HABs) in freshwater is one of the most serious contemporary environmental health concerns. Cyanobacterial HABs have become a global issue because toxins produced by some of the cyanobacteria negatively affect water sources used for drinking, recreation, aquafarming and agriculture. HABs also damage the surrounding ecosystem health. Several toxin-producing cyanobacteria release toxic metabolites (e.g. anatoxins, cylindrospermopsin, microcystins, and saxitoxin) that can cause mild to serious intoxication in animals and humans, affecting the hepatopancreatic, digestive, endocrine, dermal, and nervous systems. These toxins have also been linked to tumor promotion and death, including sudden death of pets. To protect from exposure to HABs and toxins, the dynamics and processes of cyanobacteria related to water and agricultural resources need to be clearly understood. There is relatively very little information of microbial communities and viruses with toxin dynamics in waterbodies that have chronic HAB problems during bloom seasons. In addition, research on the fate of cyanobacteria and cyanotoxin in agricultural crops has received very little attention because cyanobacteria and released cyanotoxins coexist in freshwater environments. Therefore, this dissertation seeks to understand the overall effects of cyanobacterial blooms, including Microcystis and microcystins, in freshwater and agricultural environments.Chapter 1 reviewed general information about cyanobacterial blooms, cyanotoxins, and their potential health risks. Major environmental factors associated with bloom formation and the major impact of the blooms were described including environmental, organismal, and human health perspectives. In addition, previous studies on cyanotoxin accumulation in food were summarized. In Chapter 2, to understand microbial ecology in freshwater environments during bloom season, we identified and characterized bacterial and viral communities in two lakes, Lake Erie and Buckeye Lake. An abundance of cyanobacteria and cyanotoxin producing genes were found. The concentrations of photopigments and microcystins (MCs) were also analyzed to evaluate potential health risks for human activities. This study improved understanding of cyanobacteria’s characteristics and clarified bacterial and viral interactions and structure in freshwater lakes.Chapters 3-5 focused on how cyanobacteria blooms affect agricultural environments. The major objectives of Chapter 3 were to examine the fate of microcystins (MCs) in different types of fresh produce (lettuce, carrots, and green beans), the effects of MCs on the quality and quantity of each plant, and their potential health risks. The persistence of MCs in irrigation water can lead to their transfer and accumulation in soil and agricultural plants. MC-LR accumulation levels varied by crop types and by parts of the plant (e.g., roots > shoots). The toxin persisted in the soil after harvest. MC-LR also negatively affected the quality and the crop productivity. The major objective of Chapter 4 was understanding the effects in agricultural soil after introducing cyanobacteria, especially Microcystis, via irrigation water. Introducing Microcystis in the soil affected bacterial and fungal communities (e.g. diversity, composition, and abundance), as well as crop productivity. MCs accumulated in the harvested lettuce and absorbed in the soil. Our results demonstrate that cyanobacteria colonization in agricultural soil may persistently threaten food safety and security.Lastly, Chapter 5 examined the possibility of Microcystis colonization and internalization into crops. Our results demonstrated that Microcystis can internalize via the stomata, and then adapt to the interior environments of plants. In addition, internalized Microcystis produced toxins.

Hydroponic systems have gained worldwide popularity and are increasingly used in various purposes in different geographic areas. To improve and produce more hydroponic crops, a variety of hydroponic systems have been developed, such as: wick, drip, ebb-flow, water culture, nutrient film technique, aeroponic, and windowfarm systems. Numerous studies show that hydroponics have many advantages over culture systems; i.e., reuse of water, ease in controlling external factors, and reduction of traditional farming practices (e.g., cultivating, weeding, watering, and tilling). However, limitations include: high setup cost, rapid pathogen spread, and specialized management. The purpose of this Review (Chapter 1), `Introduction to Hydroponic Systems’ are to: 1) characterize the trends, advantages, and limitations of different systems; 2) introduce different types and methods of operation; and 3) discuss research being conducted in plant diseases and the role of beneficial bacteria. The Review (Chapter 1) provides a better understanding of hydroponics and newly applied systems and discusses their optimization to enhance food quality and quantity, and reduce plant diseases. In Chapter 2, the windowfarm is described, when plants are often prone to infections by phytopathogens that slow plant growth and reduce crop productivity and excessive biofilm build-up due to high concentration of nutrients in the system. The major items discussed in Chapter 2 are: 1) development of a new windowfarm system that uses minimal water; 2) presentation of methods that promote plant health by making plants more resistant to phytopathogen infection and enhance growth using biosurfactant-producing Pseudomonas chlororaphis around plant roots; and 3) demonstration of methods that minimize biofilm build-up, such as UV irradiation, thereby extending the usable lifespan of the whole hydroponic system. To examine these items, Romaine lettuce was cultivated for 11 weeks in a windowfarm system. P. chlororaphis was inoculated near the roots, subsequently producing pyoverdine (yellow-green fluorescent pigments). For enhancing bacterial colonization, glass beads or clay granules were added. The water reservoir was treated once a week for 5 min with low pressure ultraviolet (UV) irradiation to minimize biofilm build-up in the system while maintaining the colonized beneficial microbial flora around the roots. Food productivity was measured by the number of leaves and length and weight of the lettuce; quality was measured by lettuce color. Pythium ultimum, a plant pathogen, was inoculated on the root areas to examine the protective effects of P. chlororaphis against P. ultimum. The results show that P. chlororaphis-treated lettuce grew significantly better than non-treated lettuce as indicated by enhancement of color, weight, length, and number of leaves per head (p < 0.05). The death rate of the lettuce was also reduced by half when the lettuce was treated with P. chlororaphis. UV irradiation reduced the concentration of bacteria (4 log reduction) and algae (4 log reduction) in the water reservoirs and water tubing systems. In summary, the results suggest that introduction of P. chlororaphis into a windowfarm system promotes plant growth and reduces damage caused by plant pathogens. Additionally, UV irradiation of the water reservoir results in reduction of algal and biofilm growth and extends the lifespan of the system. In Chapter 3, how the use of beneficial bacteria, addition of beads around roots and UV treatments affect bacterial diversity and community in hydroponic systems were examined. . The objectives of this study were to: 1) examine bacterial diversity and community in hydroponic systems; 2) compare the effect of three different treatments (beads, P. chlororaphis, and UV irradiation) in root areas using the PCR-DGGE method; and 3) identify bacteria in root areas and water in a windowfarm system. Bacterial profiles were compared under three different treatments (bead and P. chlororaphis treatments in root area, and UV irradiation of reservoir water) using PCR-DGGE and banding pattern analysis. After cultivation of lettuce in windowfarm systems, clay, bead and water samples were collected and bacterial community DNA was extracted for analysis. The DGGE bands were analyzed and interesting bands were selected for bacterial identification. The results demonstrated that 1) P. chlororaphis had positive effects on lettuce’s growth and root development; 2) the bacterial community of the root area was affected significantly by beads (clay pelltes versus glass beads with clay pelltes) and P. chlororaphis treatments; 3) Beads and P. chlororaphis treatments did not make the change of bacterial diversity around root area in the windowfarm system. Bacteria that are beneficial for plant growth were found in the windowfarm sytem (Variovorax paradoxus, Pseudomonas fluorescens, Pseudomonas thivervalensis, and Pseudomonas brassicacearum). In conclusion, the results suggest that 1) P. chlororaphis-treated lettuce grew significantly better than non-treated lettuce as indicated by a 50% reduction in the death rate and enhancement of color, weight, and number of leaves per head (p < 0.05); 2) UV irradiation reduced the biofilm growth in water tubing systems and extended the lifespan of the system; 3) the bacterial profile provides a better understanding of bacterial activities in the root area and water in hydroponic systems and how plants and microorganisms interact.

This research is motivated by the interest to understand how physical forces affect the configurational change of small structures. First, I report a mechanism that under an off-normal incident ion beam, ordered nanodroplets may emerge spontaneously on a solid surface. My continuum theory considers sputtering, deposition, wetting and surface energy. The simulations show that a competition between the mass supply and sputtering determines the stable size of the droplet, while the anisotropic mass flux drives the droplet to move. The balance of the flux leads to a hexagonal pattern. The shadow effect causes the droplets to line up perpendicular to the incident beam. The mechanism may be applicable to other systems to form ordered nanoscale features by self-assembly. Next, I consider individual functional structures, and use molecular dynamics simulations to investigate the effect of force on stimulus-induced deformation of rotaxane-based artificial molecular muscles. Bistable rotaxanes are composed of ring and dumbbell-shaped backbone. Upon an external stimulus, the ring switches between two recognition sites along the backbone, enabling large deformation like molecular muscles. My study shows that a small external force slows down the shuttling motion, leading to longer actuation time to full extension. Larger force significantly reduces the traveling distance of the ring and strain output. A maximum load exists which completely suppresses the shuttling motion. Last, I extend research to living structures. I use light scattering experiment to detect normal and malaria-infected blood cells. The latter are stiffer with different scattering property. By measuring the wavelength-dependent scattering at discrete angles of both forward and backward directions, I find that the signal can clearly distinguish healthy and ring stage malaria infected red blood cells. The results demonstrate elastic light scattering as a promising non-invasive diagnostic tool. In a small structure, forces of different physical origins contribute to the free energy. When the configuration changes, the free energy also changes. This free energy change defines a thermodynamic force that drives the configuration change. Insight into the process becomes increasingly valuable as the structures miniaturize. The representative systems studied in this thesis highlights the rich dynamics.