Exploring Mechanisms of Bacterial Adaptation to Seasonal Temperature Change

This research examines three potential mechanisms by which bacteria can adapt to different temperatures: changes in strain-level population structure, gene regulation and particle colonization. For the first two mechanisms, I utilize bacterial strains from the Vibrionaceae family due to their ease of culturability, ubiquity in coastal environments and status as a model system for marine bacteria. I first examine vibrio seasonal dynamics in temperate, coastal water and compare the thermal performance of strains that occupy different thermal environments. Our results suggest that there are tradeoffs in adaptation to specific temperatures and that thermal specialization can occur at a very fine phylogenetic scale. The observed thermal specialization over relatively short evolutionary time-scales indicates that few genes or cellular processes may limit expansion to a different thermal niche. I then compare the genomic and transcriptional changes associated with thermal adaptation in closely-related vibrio strains under heat and cold stress. The two vibrio strains have very similar genomes and overall exhibit similar transcriptional profiles in response to temperature stress but their temperature preferences are determined by differential transcriptional responses in shared genes as well as temperature-dependent regulation of unique genes. Finally, I investigate the temporal dynamics of particle-attached and free-living bacterial community in coastal seawater and find that microhabitats exert a stronger forcing on microbial communities than environmental variability, suggesting that particle-attachment could buffer the impacts of environmental changes and particle-associated communities likely respond to the presence of distinct eukaryotes rather than commonly-measured environmental parameters. Integrating these results will offer new perspectives on the mechanisms by which bacteria respond to seasonal temperature changes as well as potential adaptations to climate change-driven warming of the surface oceans.

Passive Acoustics: A Multifaceted Tool for Marine Mammal Conservation

Marine mammals exploit the efficiency of sound propagation in the marine environment for essential activities like communication and navigation. For this reason, passive acoustics has particularly high potential for marine mammal studies, especially those aimed at population management and conservation. Despite the rapid realization of this potential through a growing number of studies, much crucial information remains unknown or poorly understood. This research attempts to address two key knowledge gaps, using the well-studied bottlenose dolphin (Tursiops truncatus) as a model species, and underwater acoustic recordings collected on four fixed autonomous sensors deployed at multiple locations in Sarasota Bay, Florida, between September 2012 and August 2013. Underwater noise can hinder dolphin communication. The ability of these animals to overcome this obstacle was examined using recorded noise and dolphin whistles. I found that bottlenose dolphins are able to compensate for increased noise in their environment using a wide range of strategies employed in a singular fashion or in various combinations, depending on the frequency content of the noise, noise source, and time of day. These strategies include modifying whistle frequency characteristics, increasing whistle duration, and increasing whistle redundancy. Recordings were also used to evaluate the performance of six recently developed passive acoustic abundance estimation methods, by comparing their results to the true abundance of animals, obtained via a census conducted within the same area and time period. The methods employed were broadly divided into two categories – those involving direct counts of animals, and those involving counts of cues (signature whistles). The animal-based methods were traditional capture-recapture, spatially explicit capture-recapture (SECR), and an approach that blends the “snapshot” method and mark-recapture distance sampling, referred to here as (SMRDS). The cue-based methods were conventional distance sampling (CDS), an acoustic modeling approach involving the use of the passive sonar equation, and SECR. In the latter approach, detection probability was modelled as a function of sound transmission loss, rather than the Euclidean distance typically used. Of these methods, while SMRDS produced the most accurate estimate, SECR demonstrated the greatest potential for broad applicability to other species and locations, with minimal to no auxiliary data, such as distance from sound source to detector(s), which is often difficult to obtain. This was especially true when this method was compared to traditional capture-recapture results, which greatly underestimated abundance, despite attempts to account for major unmodelled heterogeneity. Furthermore, the incorporation of non-Euclidean distance significantly improved model accuracy. The acoustic modelling approach performed similarly to CDS, but both methods also strongly underestimated abundance. In particular, CDS proved to be inefficient. This approach requires at least 3 sensors for localization at a single point. It was also difficult to obtain accurate distances, and the sample size was greatly reduced by the failure to detect some whistles on all three recorders. As a result, this approach is not recommended for marine mammal abundance estimation when few recorders are available, or in high sound attenuation environments with relatively low sample sizes. It is hoped that these results lead to more informed management decisions, and therefore, more effective species conservation.

The Effects of Organic Matter Amendments and Migratory Waterfowl on Greenhouse Gas and Nutrient Dynamics in Managed Coastal Plain Wetlands

Wetland ecosystems provide many valuable ecosystem services, including carbon (C) storage and improvement of water quality. Yet, restored and managed wetlands are not frequently evaluated for their capacity to function in order to deliver on these values. Specific restoration or management practices designed to meet one set of criteria may yield unrecognized biogeochemical costs or co-benefits. The goal of this dissertation is to improve scientific understanding of how wetland restoration practices and waterfowl habitat management affect critical wetland biogeochemical processes related to greenhouse gas emissions and nutrient cycling. I met this goal through field and laboratory research experiments in which I tested for relationships between management factors and the biogeochemical responses of wetland soil, water, plants and trace gas emissions. Specifically, I quantified: (1) the effect of organic matter amendments on the carbon balance of a restored wetland; (2) the effectiveness of two static chamber designs in measuring methane (CH4) emissions from wetlands; (3) the impact of waterfowl herbivory on the oxygen-sensitive processes of methane emission and coupled nitrification-denitrification; and (4) nitrogen (N) exports caused by prescribed draw down of a waterfowl impoundment.

The potency of CH4 emissions from wetlands raises the concern that widespread restoration and/or creation of freshwater wetlands may present a radiative forcing hazard. Yet data on greenhouse gas emissions from restored wetlands are sparse and there has been little investigation into the greenhouse gas effects of amending wetland soils with organic matter, a recent practice used to improve function of mitigation wetlands in the Eastern United States. I measured trace gas emissions across an organic matter gradient at a restored wetland in the coastal plain of Virginia to test the hypothesis that added C substrate would increase the emission of CH4. I found soils heavily loaded with organic matter emitted significantly more carbon dioxide than those that have received little or no organic matter. CH4 emissions from the wetland were low compared to reference wetlands and contrary to my hypothesis, showed no relationship with the loading rate of added organic matter or total soil C. The addition of moderate amounts of organic matter (< 11.2 kg m-2) to the wetland did not greatly increase greenhouse gas emissions, while the addition of high amounts produced additional carbon dioxide, but not CH4.

I found that the static chambers I used for sampling CH4 in wetlands were highly sensitive to soil disturbance. Temporary compression around chambers during sampling inflated the initial chamber CH4 headspace concentration and/or lead to generation of nonlinear, unreliable flux estimates that had to be discarded. I tested an often-used rubber-gasket sealed static chamber against a water-filled-gutter seal chamber I designed that could be set up and sampled from a distance of 2 m with a remote rod sampling system to reduce soil disturbance. Compared to the conventional design, the remotely-sampled static chambers reduced the chance of detecting inflated initial CH4 concentrations from 66 to 6%, and nearly doubled the proportion of robust linear regressions from 45 to 86%. The new system I developed allows for more accurate and reliable CH4 sampling without costly boardwalk construction.

I explored the relationship between CH4 emissions and aquatic herbivores, which are recognized for imposing top-down control on the structure of wetland ecosystems. The biogeochemical consequences of herbivore-driven disruption of plant growth, and in turn, mediated oxygen transport into wetland sediments, were not previously known. Two growing seasons of herbivore exclusion experiments in a major waterfowl overwintering wetland in the Southeastern U.S. demonstrate that waterfowl herbivory had a strong impact on the oxygen-sensitive processes of CH4 emission and nitrification. Denudation by herbivorous birds increased cumulative CH4 flux by 233% (a mean of 63 g CH4 m-2 y-1) and inhibited coupled nitrification-denitrification, as indicated by nitrate availability and emissions of nitrous oxide. The recognition that large populations of aquatic herbivores may influence the capacity for wetlands to emit greenhouse gases and cycle nitrogen is particularly salient in the context of climate change and nutrient pollution mitigation goals. For example, our results suggest that annual emissions of 23 Gg of CH4 y-1 from ~55,000 ha of publicly owned waterfowl impoundments in the Southeastern U.S. could be tripled by overgrazing.

Hydrologically controlled moist-soil impoundment wetlands provide critical habitat for high densities of migratory bird populations, thus their potential to export nitrogen (N) to downstream waters may contribute to the eutrophication of aquatic ecosystems. To investigate the relative importance of N export from these built and managed habitats, I conducted a field study at an impoundment wetland that drains into hypereutrophic Lake Mattamuskeet. I found that prescribed hydrologic drawdowns of the impoundment exported roughly the same amount of N (14 to 22 kg ha-1) as adjacent fertilized agricultural fields (16 to 31 kg ha-1), and contributed approximately one-fifth of total N load (~45 Mg N y-1) to Lake Mattamuskeet. Ironically, the prescribed drawdown regime, designed to maximize waterfowl production in impoundments, may be exacerbating the degradation of habitat quality in the downstream lake. Few studies of wetland N dynamics have targeted impoundments managed to provide wildlife habitat, but a similar phenomenon may occur in some of the 36,000 ha of similarly-managed moist-soil impoundments on National Wildlife Refuges in the southeastern U.S. I suggest early drawdown as a potential method to mitigate impoundment N pollution and estimate it could reduce N export from our study impoundment by more than 70%.

In this dissertation research I found direct relationships between wetland restoration and impoundment management practices, and biogeochemical responses of greenhouse gas emission and nutrient cycling. Elevated soil C at a restored wetland increased CO2 losses even ten years after the organic matter was originally added and intensive herbivory impact on emergent aquatic vegetation resulted in a ~230% increase in CH4 emissions and impaired N cycling and removal. These findings have important implications for the basic understanding of the biogeochemical functioning of wetlands and practical importance for wetland restoration and impoundment management in the face of pressure to mitigate the environmental challenges of global warming and aquatic eutrophication.

Identifying the Structure and Fate of Wastewater Derived Organic Micropollutants by High-resolution Mass Spectrometry

Human activities represent a significant burden on the global water cycle, with large and increasing demands placed on limited water resources by manufacturing, energy production and domestic water use. In addition to changing the quantity of available water resources, human activities lead to changes in water quality by introducing a large and often poorly-characterized array of chemical pollutants, which may negatively impact biodiversity in aquatic ecosystems, leading to impairment of valuable ecosystem functions and services. Domestic and industrial wastewaters represent a significant source of pollution to the aquatic environment due to inadequate or incomplete removal of chemicals introduced into waters by human activities. Currently, incomplete chemical characterization of treated wastewaters limits comprehensive risk assessment of this ubiquitous impact to water. In particular, a significant fraction of the organic chemical composition of treated industrial and domestic wastewaters remains uncharacterized at the molecular level. Efforts aimed at reducing the impacts of water pollution on aquatic ecosystems critically require knowledge of the composition of wastewaters to develop interventions capable of protecting our precious natural water resources.

The goal of this dissertation was to develop a robust, extensible and high-throughput framework for the comprehensive characterization of organic micropollutants in wastewaters by high-resolution accurate-mass mass spectrometry. High-resolution mass spectrometry provides the most powerful analytical technique available for assessing the occurrence and fate of organic pollutants in the water cycle. However, significant limitations in data processing, analysis and interpretation have limited this technique in achieving comprehensive characterization of organic pollutants occurring in natural and built environments. My work aimed to address these challenges by development of automated workflows for the structural characterization of organic pollutants in wastewater and wastewater impacted environments by high-resolution mass spectrometry, and to apply these methods in combination with novel data handling routines to conduct detailed fate studies of wastewater-derived organic micropollutants in the aquatic environment.

In Chapter 2, chemoinformatic tools were implemented along with novel non-targeted mass spectrometric analytical methods to characterize, map, and explore an environmentally-relevant “chemical space” in municipal wastewater. This was accomplished by characterizing the molecular composition of known wastewater-derived organic pollutants and substances that are prioritized as potential wastewater contaminants, using these databases to evaluate the pollutant-likeness of structures postulated for unknown organic compounds that I detected in wastewater extracts using high-resolution mass spectrometry approaches. Results showed that application of multiple computational mass spectrometric tools to structural elucidation of unknown organic pollutants arising in wastewaters improved the efficiency and veracity of screening approaches based on high-resolution mass spectrometry. Furthermore, structural similarity searching was essential for prioritizing substances sharing structural features with known organic pollutants or industrial and consumer chemicals that could enter the environment through use or disposal.

I then applied this comprehensive methodological and computational non-targeted analysis workflow to micropollutant fate analysis in domestic wastewaters (Chapter 3), surface waters impacted by water reuse activities (Chapter 4) and effluents of wastewater treatment facilities receiving wastewater from oil and gas extraction activities (Chapter 5). In Chapter 3, I showed that application of chemometric tools aided in the prioritization of non-targeted compounds arising at various stages of conventional wastewater treatment by partitioning high dimensional data into rational chemical categories based on knowledge of organic chemical fate processes, resulting in the classification of organic micropollutants based on their occurrence and/or removal during treatment. Similarly, in Chapter 4, high-resolution sampling and broad-spectrum targeted and non-targeted chemical analysis were applied to assess the occurrence and fate of organic micropollutants in a water reuse application, wherein reclaimed wastewater was applied for irrigation of turf grass. Results showed that organic micropollutant composition of surface waters receiving runoff from wastewater irrigated areas appeared to be minimally impacted by wastewater-derived organic micropollutants. Finally, Chapter 5 presents results of the comprehensive organic chemical composition of oil and gas wastewaters treated for surface water discharge. Concurrent analysis of effluent samples by complementary, broad-spectrum analytical techniques, revealed that low-levels of hydrophobic organic contaminants, but elevated concentrations of polymeric surfactants, which may effect the fate and analysis of contaminants of concern in oil and gas wastewaters.

Taken together, my work represents significant progress in the characterization of polar organic chemical pollutants associated with wastewater-impacted environments by high-resolution mass spectrometry. Application of these comprehensive methods to examine micropollutant fate processes in wastewater treatment systems, water reuse environments, and water applications in oil/gas exploration yielded new insights into the factors that influence transport, transformation, and persistence of organic micropollutants in these systems across an unprecedented breadth of chemical space.

Strategies for Coping with Multiple Biological Safety Regulations in High-Containment Laboratories

The increase in biological safety regulations and/or guidelines regarding personnel and facilities in high containment laboratories demands constant vigilance by biological safety professionals responsible for safety in these environments. Safety professionals have been faced with legislative compliance issues in the past and have developed effective management methods to cope with the demands of these requirements. Examples include the impact of the National Institutes of Health (NIH) recombinant DNA (rDNA) Guidelines and the Occupational Safety and Health Administration's (OSHA) Bloodborne Pathogens Standard. This chapter will attempt to describe seven successful strategies for management of regulatory compliance in research that are based on an overall philosophy of developing a “culture of safety”. Strategies range from interactive involvement with administration and research staff to biological safety professional development.

Advanced Aerogel Composites for Oil Remediation and Recovery

Oil spills in marine environments often damage marine and coastal life if not remediated rapidly and efficiently. In spite of the strict enforcement of environmental legislations (i.e., Oil Pollution Act 1990) following the Exxon Valdez oil spill (June 1989; the second biggest oil spill in U.S. history), the Macondo well blowout disaster (April 2010) released 18 times more oil. Strikingly, the response methods used to contain and capture spilled oil after both accidents were nearly identical, note that more than two decades separate Exxon Valdez (1989) and Macondo well (2010) accidents.

The goal of this dissertation was to investigate new advanced materials (mechanically strong aerogel composite blankets-Cabot® Thermal Wrap™ (TW) and Aspen Aerogels® Spaceloft® (SL)), and their applications for oil capture and recovery to overcome the current material limitations in oil spill response methods. First, uptake of different solvents and oils were studied to answer the following question: do these blanket aerogel composites have competitive oil uptake compared to state-of-the-art oil sorbents (i.e., polyurethane foam-PUF)? In addition to their competitive mechanical strength (766, 380, 92 kPa for Spaceloft, Thermal Wrap, and PUF, respectively), our results showed that aerogel composites have three critical advantages over PUF: rapid (3-5 min.) and high (more than two times of PUF’s uptake) oil uptake, reusability (over 10 cycles), and oil recoverability (up to 60%) via mechanical extraction. Chemical-specific sorption experiments showed that the dominant uptake mechanism of aerogels is adsorption to the internal surface, with some contribution of absorption into the pore space.

Second, we investigated the potential environmental impacts (energy and chemical burdens) associated with manufacturing, use, and disposal of SL aerogel and PUF to remove the oil (i.e., 1 m3 oil) from a location (i.e., Macondo well). Different use (single and multiple use) and end of life (landfill, incinerator, and waste-to-energy) scenarios were assessed, and our results demonstrated that multiple use, and waste-to-energy choices minimize the energy and material use of SL aerogel. Nevertheless, using SL once and disposing via landfill still offers environmental and cost savings benefits relative to PUF, and so these benefits are preserved irrespective of the oil-spill-response operator choices.

To inform future aerogel manufacture, we investigated the different laboratory-scale aerogel fabrication technologies (rapid supercritical extraction (RSCE), CO2 supercritical extraction (CSCE), alcohol supercritical extraction (ASCE)). Our results from anticipatory LCA for laboratory-scaled aerogel fabrication demonstrated that RSCE method offers lower cumulative energy and ecotoxicity impacts compared to conventional aerogel fabrication methods (CSCE and ASCE).

The final objective of this study was to investigate different surface coating techniques to enhance oil recovery by modifying the existing aerogel surface chemistries to develop chemically responsive materials (switchable hydrophobicity in response to a CO2 stimulus). Our results showed that studied surface coating methods (drop casting, dip coating, and physical vapor deposition) were partially successful to modify surface with CO2 switchable chemical (tributylpentanamidine), likely because of the heterogeneous fiber structure of the aerogel blankets. A possible solution to these non-uniform coatings would be to include switchable chemical as a precursor during the gel preparation to chemically attach the switchable chemical to the pores of the aerogel.

Taken as a whole, the implications of this work are that mechanical deployment and recovery of aerogel composite blankets is a viable oil spill response strategy that can be deployed today. This will ultimately enable better oil uptake without the uptake of water, potential reuse of the collected oil, reduced material and energy burdens compared to competitive sorbents (e.g., PUF), and reduced occupational exposure to oiled sorbents. In addition, sorbent blankets and booms could be deployed in coastal and open-ocean settings, respectively, which was previously impossible.