Coral diseases were first noted in the 1960s and 1970s and have had major impacts globally on coral reef community structures. In the Caribbean, a major outbreak of white band disease has been considered responsible for the drastic decline of Caribbean Acroporids since the 1970s. In addition to white band disease, another more recently described condition known as rapid tissue loss (RTL) has had major impacts on Acropora cervicornis populations, specifically offshore Broward County Southeast Florida. While these diseases have contributed to the population decline, determining their etiologies has been elusive. Coral diseases have been characterized by shifts in their microbial counterparts within many levels of the coral host. While some coral diseases have had specific pathogens identified, research has not been able to determine pathogens for most. Evidence points toward bacterial causes for many diseases, but due to the complexity of the coral holobiont and the interaction with the environment, elucidating the causes has proven difficult. Many studies have examined the microbiomes of specific diseases and determined some potential pathogens or at least taxa playing important roles in the disease, although none have looked at RTL. Recognizing the local affect of RTL on A. cervicornis, this study set out to gain a baseline understanding of the healthy and RTL affected microbiome of A. cervicornis. 16S rRNA gene sequencing was used to examine the microbiome of completely healthy colonies, healthy regions of diseased colonies, and the disease margin of diseased colonies. Analysis of four microbial diversity metrics revealed marked increases in diversity with respect to declining health states. Additionally, community dissimilarity analysis and analysis of differentially abundant taxa exhibited distinct microbial community structures due to coral health. Several highly abundant (Rickettsiales, Rhodobacteraceae) and a few low abundance (Bdellovibrionales) taxa were identified as primary drivers of the differences. Additionally, Piscirickettsiaceae, a known fish pathogen, was consistently associated with RTL and warrants further investigation. All of the taxa identified with in RTL have been associated with other Acroporid and non-Acroporid diseases throughout the Caribbean and the rest of the world. The consistent IV association of similar taxa for coral diseases around the world, including those found in this study, supports the recent ideas of non-specific primary pathogens. While most disease studies, coral and otherwise, aim to determine a single pathogen for a single disease, this study and others suggest there could be a multitude of organisms responsible for the disease. Therefore understanding the interactions of the coral holobiont and the environment is important to understanding coral disease. While this study reveals significant changes in the bacterial community associated with RTL as well as some potential pathogens, the relationships appear complex and perhaps at a functional level rather than merely taxonomic. Furthermore, this study did not examine viruses, fungi, or protists, which could be possible pathogens. Therefore, to further develop an understanding of RTL and many other coral diseases it will be necessary to consider additional none-bacterial members of the holobiont as well as the bacterial functions and taxa coupled with the roles of environmental factors.

Harmful algal blooms (HABs) are found worldwide, particularly in places where warm, well-lit, and stagnant waters are common. HABs can have negative effects on aquatic plants and wildlife due to the reduction in light availability associated with turbidity, decrease in O2 availability, and the production of secondary metabolites that can harm or even prove lethal. Aquatic ecosystems are regularly being affected by elevated salinity because of recent water management strategies, episodes of drought, and salt water intrusion. This research focused on how salinity levels ranging from 0-10ppt affected physiological attributes such as cellular growth and abundance, cell mortality, toxin release, and oxidative stress in the toxigenic cyanobacterium, Microcystis aeruginosa. It was determined that salinity treatments of 7ppt and above caused a decrease in both cellular growth and abundance, as well as an increase in toxin release due to cell mortality. M. aeruginosa was able to survive in salinities up to 7ppt. A pattern of caspase activity in response to elevated salinity was shown, but whether cellular mortality was due solely to programmed cell death (PCD) was not definitive. A strong antioxidant response, measured through catalase activity, was noted when salinity was enhanced to 7ppt. Above this value, the damaging effects of salinity caused elevated levels of reactive oxygen species (ROS) production and cell death. It was determined that the maximum amount of hydrogen peroxide that M. aeruginosa could withstand without significant impact to growth and abundance was below 250µM. Salinities of 7ppt and above had a negative impact on the physiology of M. aeruginosa, leading to cell death and an increase in microcystin release into the environment. These two factors can lead to fish kills, poor drinking water, and other recreational and commercial problems for an aquatic ecosystem. By determining the precise salinity that HAB cellular mortality is imminent, predictive models can be employed to predict the impacts of salt intrusion and groundwater management.

Pine rocklands are endangered ecosystems unique to south Florida, the Bahamas and Cuba. As a result of their karstic calcium carbonate­rich soil, these systems are limited in phosphorus and nitrogen, making symbiotic associations critical to plant growth. Four leguminous species (Cajanus cajan, Chamaecrista fasciculata, Tephrosia angustissima, and Abrus precatorious) were used to determine the relationship between rhizobial partners and plant performance, and the symbiosis related gene nifH was amplified to characterize the diversity of rhizobial symbionts. Plants were grown in soils from four different south Florida pine rocklands, and a salinity treatment was added to determine how storm surge and sea level rise could affect this symbiotic relationship. While plant performance and nodulation were highly impacted by soil type, salinity did not represent a significant effect. Phylogenetic analysis determined that all four plant species were found to associate with Bradyrhizobium spp. and no rhizobial shift between salinity treatment and soil type was found.

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Microalgae can be grown on municipal wastewater media to both treat the wastewater and produce feedstock for algae biofuel production. However the reliability of treatment must be demonstrated, as well as high areal algae productivity on recycled wastewater media and efficient sedimentation harvesting. This processes was studied at pilot scale in the present research. A pilot facility was operated with nine CO2-supplemented raceway ponds, each with a 33-m2 surface area and a 0.3-m depth, continuously from March 6, 2013 through September 24, 2014. The ponds were operated as three sets of triplicates with two sets continuously fed primary-clarified municipal wastewater at either a 2-day or 3-day hydraulic residence time (HRT), and one set fed the clarified effluent of the 3-day pond set. This second pond-in-series was operated with a 3-day HRT. Areal biomass productivity is reported as gross and net, the former based only on biomass in the pond effluents and the latter subtracting the volatile suspended solids in the influent from those in the effluent. An estimate was also made of autotrophic biomass productivity, as differentiated from heterotrophic growth. Over a year, net productivity averaged 83 metric tons per hectare per year (MT/ha-yr) for the 2-day HRT ponds, 52 MT/ha-yr for the 3-day HRT ponds, and 44 MT/ha-yr for the 3-day HRT ponds receiving clarified effluent of the first set of 3-day HRT ponds (i.e., recycled water). The lower net productivity of the pond receiving water recycling was attributed to two factors. First, the relatively high influent suspended solids concentrations were subtracted from the effluent suspended solids concentrations before net productivity was calculated. Second, the recycled water contained less soluble organic matter than the primary-clarified wastewater leading to less heterotrophic biomass production. The accumulation of inhibitory allelochemicals is a possible third cause of lower productivity , but no specific information was collected on allelopathy. Algae were harvested from pond effluent by sedimentation, with harvest efficiency most affected by the extent of natural bioflocculation occurring in the ponds. Some forms of bioflocculation are thought to be mediated by bacteria, which often make-up a substantial fraction of the settled flocs. Pond samples settled in 1-L Imhoff cones averaged/L total suspended solids after 24 hours of settling; but all ponds fell short of meeting an averaged/L total suspended solids after a 2 hour interval which would be ideally achieved for wastewater effluent. No relationship was seen between settling performance and the bacterial content of flocs. Soluble carbonaceous biochemical oxygen demand (scBOD5) removal by the raceway ponds was sufficient to meet wastewater treatment requirements year around. Influent scBOD5 concentrations averaged 83 mg/L, and the effluent averaged 5.1 mg/L and 4.2 mg/L for the 2-day and 3-day HRT pond sets, respectively. The variable with the greatest influence on productivity in all pond sets, and settling performance in the recycled water pond set, was season (i.e., co-correlated variables of solar insolation and pond temperature). Neither productivity nor settling appeared to be related to prominent algae genera or prevalence of grazers. The high net productivity achieved with a growth medium of primary clarifier effluent and the generally high settleability of algal-bacterial flocs indicate a good potential for algae wastewater treatment and biofuel production. However, the settling of algae grown on recycled water needs improvement to achieve the full potential of wastewater-grown algae biofuel production.

Microalgae are considered one of the most promising feedstocks for biofuel production for the future. The most efficient way to produce vast amounts of algal biomass is the use of closed tubular photobioreactors (PBR). The heat requirement for a given system is a major concern since the best algae growth rates are obtained between 25-30 °C, depending on the specific strain. A procedure to determine temperature influence on algal growth rates was developed for a lab-scale PBR system using the species Chlorella. A maximum growth rate of 1.44 doublings per day at 29 °C (optimal temperature) was determined. In addition, a dynamic mathematical model was developed to simulate heating and cooling energy requirements of tubular PBRs for any desired location. Operating the model with hourly weather data as input, heating and cooling loads can be calculated early in the planning stage of a project. Furthermore, the model makes it possible to compare the operation inside a greenhouse to the outdoor operations, and consequently provides fundamental information for an economic feasibility study. The best configuration for a specific location can be evaluated easily. The model was exemplary tested for a hypothetical 100,000 l photobioreactor located in San Luis Obispo, California, U.S.A. Average algae productivity rates of 23% and 67% for outdoor and indoor PBR operations, respectively, were obtained. Actual energy loads (heating and cooling) needed to maintain the PBR at optimal temperature were determined and compared. Sensitivity analyses had been performed for abrupt temperature and solar radiation steps, PBR row distances, ground reflectivities, and ventilation rates of the greenhouse. An optimal row distance of 0.75 m was determined for the specific PBR. The least amount of energy was needed for a ground reflectivity of 20%. The ventilation rate had no major influence on the productivity rate of the system. Results demonstrated the importance of a simulation model as well as the economic impact of a sophisticated heat management system. Energy savings due to an optimized heat management system will eventually increase proficiency of the systems, which will support a new sustainable industry and future developmental potential.

The transition of natural landscapes to intensive agricultural uses has resulted in severe loss of soil organic carbon (SOC), increased CO₂ emissions, river depletion, and groundwater overdraft. Despite negative documented effects of agricultural land use (i.e., soil erosion, nutrient runoff) on critical natural resources (i.e., water, soil), food production must increase to meet the demands of a rising human population. Given the environmental and agricultural productivity concerns of intensely managed soils, it is critical to implement conservation practices that mitigate the negative effects of crop production and enhance environmental integrity. In the Mississippi Alluvial Valley (MAV) region of Mississippi, USA, the adoption of cover crop (CC) and no-tillage (NT) management practices has been low because of a lack of research specific to the regional nuances. Therefore, this study assessed the long-term soil physiochemical and biological responses from integrating CC and NT management to agricultural soils of the region. Research plots were established in a split-block design with two tillage treatments: NT and reduced tillage (RT) and three CC treatments: no cover (NC), rye (RY) and a rye+clover (RC) mix. Soil samples were taken during the growing season of 2019 and 2020. Bulk density was found to be significantly lower in NT plots and aggregate stability was greatest in plots with a single CC species. Moisture retention increased in NT.. Soil organic carbon was greater in NT and CC treatments and there was no difference in CO₂ flux. Bacterial abundance had a positive effect on SOC but a negative effect on CO₂. The rate of proportional change and pattern of variability in C pools suggested loss of SOC in reduced tillage (RT) treatments. Microbial abundance, functional genes and enzyme activity was greater in NT with CC, but diversity was greater in RT. No-tillage practices lower diversity and influence long-term community changes while CC practices enact a seasonal response to environmental conditions. I conclude that in heavy clay soils of the mid-South region of the MAV, RT with a CC is optimal for soil health traits associated with crop sustainability, however the management will still contribute to increased CO₂ emissions.

The contamination of the environment, accidental or intentional, in particular with chemical toxins such as industrial chemicals and chemical warfare agents has increased public fear. There is a critical requirement for the continuous detection of toxins present at very low levels in the environment. Indeed, some ultra-sensitive analytical techniques already exist, for example chromatography and mass spectroscopy, which are approved by the US Environmental Protection Agency for the detection of toxins. However, these techniques are limited to the detection of known toxins. Cellular expression of genomic and proteomic biomarkers in response to toxins allows monitoring of known as well as unknown toxins using Polymerase Chain Reaction and Enzyme Linked Immunosensor Assays. However, these molecular assays allow only the endpoint (extracellular) detection and use labels such as fluorometric, colorimetric and radioactive, which increase chances of uncertainty in detection. Additionally, they are time, labor and cost intensive. These technical limitations are unfavorable towards the development of a biosensor technology for continuous detection of toxins. Federal agencies including the Departments of Homeland Security, Agriculture, Defense and others have urged the development of a detect-to-protect class of advanced biosensors, which enable environmental surveillance of toxins in resource-limited settings. In this study a Surface-Enhanced Raman Spectroscopy (SERS) immunosensor, aka a SERS-linked immunosensor assay (SLISA), has been developed. Colloidal silver nanoparticles (Ag NPs) were used to design a flexible SERS immunosensor. The SLISA proof-of-concept biosensor was validated by the measurement of a dose dependent expression of RAD54 and HSP70 proteins in response to H2O2 and UV. A prototype microchip, best suited for SERS acquisition, was fabricated using an on-chip SLISA to detect RAD54 expression in response to H2O2. A dose-response relationship between H2O2 and RAD54 is established and correlated with EPA databases, which are established for human health risk assessment in the events of chemical exposure. SLISA outperformed ELISA by allowing RISE (rapid, inexpensive, simple and effective) detection of proteins within 2 hours and 3 steps. It did not require any label and provided qualitative information on antigen-antibody binding. SLISA can easily be translated to a portable assay using a handheld Raman spectrometer and it can be used in resource-limited settings. Additionally, this is the first report to deliver Ag NPs using TATHA2, a fusogenic peptide with cell permeability and endosomal rupture release properties, for rapid and high levels of Ag NPs uptake into yeast without significant toxicity, prerequisites for the development of the first intracellular SERS immunosensor.

Lilium grayi (Gray’s Lily), a southern Appalachian endemic species, is threatened by a Lilium-specific fungal pathogen, Pseudocercosporella inconspicua. The disease is characterized by tan lesions that can cause early senescence, while also lowering seed production and viability. This project tested for P. inconspicua conidia and accessed health at nine locations. The disease was present and ubiquitous across the range of L. grayi. Through identification of P. inconspicua conidia in the field, L. superbum (Turk’s Cap Lily) was identified as an additional host, while L. michauxii (Michaux’s Lily) was disease-free. However, infection was inducible in both species. With the disease widespread in L. superbum and this species represented by many large populations, L. superbum may act as disease reservoir, further complicating the outlook for L. grayi. The disease should be considered an epidemic because of its impact on individual plants, its commonness within populations, and its ubiquity across the geographical range.

Food borne illnesses continues to be a public health challenge in the United States (U.S.); an estimated 9.4 million incident cases occurred in 2011. In view of this challenge we conducted two food safety studies; 1) related to product formulation (hummus spoilage challenge study) and 2) evaluating the microbial safety of domestic kitchen surfaces in Residential Child Care Institutions (RCCI pilot study). Hummus is of Mediterranean origin but is currently eaten globally. This challenge study evaluates a variety of industrial hummus formulations (four in total, differing in pH and/or addition of a preservative (natamycin). Two batches were setup: batch 1; aseptically inoculated hummus with 100 CFU/g fungal isolates and batch 2; uninoculated hummus. Samples of both hummus batches were stored at both 20oC (10 days accelerated testing) and 4oC (84 days recommended temperature testing). Inoculated samples were analyzed for fungus, whiles both fungi and bacteria (standard plate count (SPC) and Lactococci) counts were done for uninoculated samples. Results indicate that accelerated testing inaccurately predicts fungal growth at 4oC in hummus, also fungal growth inhibition requires a pH ≤ 4.0 ± 0.2 and refrigeration. Limited studies have specifically evaluated the prevalence of pathogenic bacteria in domestic kitchens in the U.S, for this reason we assessed the microbial safety of 6 RCCI locations in MA. Fifteen key food contact surfaces and dish washing sponges, if available at each RCCI facility were assessed for SPC, yeast and molds, total coliform and E. coli, Listeria sp and Salmonella sp. Microbiological assessments were conducted preceding and after a hazard analysis and critical control point (HACCP) food safety training and implementation at each location. Microbial growth varied by surface for each type of microorganism, wet surfaces had higher most probable number (MPN) counts. Compared to dry surfaces, wet surfaces had significantly higher mean total coliform counts. For both E. coli and total coliform, microbial load differed significantly by surfaces sampled (P = 0.0323 and 0.014) respectively. The surface and training interaction effect was highly significant for only E. coli (P = 0.0089). Training overall had no significant effect on reducing the microbial load on kitchen surfaces.