Browsing by Subject "Biodegradation"
Results Per Page
Sort Options
Item Embargo Advancing Polyhydroxyalkanoate Biopolymer Material Design: Integrating Machine Learning and Experimental Validation(2024) Lalonde, Jessica NicoleVirtually every consumer product available on the market today contains some form of fossil fuel-based polymer. However, these materials pose environmental, human health, and economic concerns due to their enduring presence in the global ecosystem and their degradation products. Addressing this crisis necessitates scalable production of biodegradable alternatives, such as polyhydroxyalkanoates (PHAs). PHAs are presented as promising substitutes due to their biodegradability, biocompatibility, and the potential for complete renewable utilization post-degradation, but a current challenge to widespread use of these materials lies in understanding the quantitative relationship between the structural characteristics of PHAs, their environmental interactions, and their degradation rates to enhance their industrial production and distribution. To bridge this knowledge gap, the dissertation outlines a comprehensive approach involving the development of a specialized dataset, the application of machine learning (ML) models to predict degradation rates based on structural and environmental factors, and the experimental validation of these predictions. The first part of this research focuses on assembling a manually curated dataset from the extensive, available open-access literature, aimed at understanding the effects of structural and environmental features on PHA degradation. The second part leverages this dataset through ML modeling, employing techniques like random forest regression to predict degradation profiles with over 80% accuracy. This methodology enables a deeper understanding of the complex interplay between chemical structures and degradation properties, surpassing traditional trial-and-error approaches. The final part of this research aims to complete an iterative workflow for dataset development by validating ML model predictions through physical experiments, enriching the original dataset with comprehensive experimental data on PHA degradation in hydrolytic environments with contact angle, molecular weight, and thermal property characterizations. The incorporation of experimental findings into the ML dataset, particularly through expanded ML techniques that emphasize pairwise feature importance such as explainable boosting machines (EBM), helps in pinpointing critical factors influencing PHA degradation, such as environmental temperature and material properties. The model performances indicate a strong performance of manually assembled literature-based datasets when predicting degradation rate for PHAs. In conclusion, a data science-based framework has been developed for exploring PHA biopolyester degradation and explores the combination of features of the material and its environment that integrates the structure, properties, and experimentally verified degradation profiles of the material. This workflow will be a useful and generalizable pipeline for PHAs and other polymers to expand the biopolymer design space with degradation in mind.
Item Open Access Biodegradation of a Sulfur-Containing PAH, Dibenzothiophene, by a Mixed Bacterial Community(2009) Cooper, Ellen M.Dibenzothiophene (DBT) is a constituent of creosote and petroleum waste contamination, it is a model compound for more complex thiophenes, and its degradation by mixed microbial communities has received little attention. The chemical characteristics, environmental fate and ecotoxicology of DBT degradation products are not well understood. This research investigated DBT degradation in an enrichment culture derived from creosote-contaminated estuarian sediment using a suite of assays to monitor bacterial populations, bacterial growth, degradation products, DBT loss, and toxicity. Ultraviolet (UV) irradiation was evaluated as a sequential treatment following biodegradation. Additionally, to advance SYBR-Green qPCR methodology for characterizing mixed microbial communities, an alternative approach for evaluating qPCR data using a sigmoidal model to fit the amplification curve was compared to the conventional approach in artificial mixed communities. The overall objective of this research was to gain a comprehensive understanding of the degradation of a model heterocyclic PAH, DBT, by a mixed microbial community, particularly within the context of remediation goals.
DBT biodegradation was evaluated in laboratory scale cultures with and without pH control. The microbial community was monitored with 10 primer sets using SYBR-Green quantitative polymerase chain reaction (qPCR). Twenty-seven degradation products were identified by gas chromatography and mass spectrometry (GC/MS). The diversity of these products indicated that multiple pathways functioned in the community. DBT degradation appeared inhibited under acidic conditions. Toxicity to bioluminescent bacteria Vibrio fischeri more than doubled in the first few days of degradation, was never reduced below initial levels, and was attributed in part to one or more degradation products. UV treatment following biodegradation was explored using a monochromatic (254 nm) low-pressure UV lamp. While DBT was not extensively photooxidized, several biodegradation products were susceptible to UV treatment. At higher doses, UV treatment following DBT biodegradation exacerbated cardiac defects in Fundulus heteroclitus embryos, but slightly reduced toxicity to V. fischeri.
This research provides a uniquely comprehensive view of the DBT degradation process, identifying bacterial populations previously unassociated with PAH biodegradation, as well as potentially hazardous products that may form during biodegradation. Additionally, this research contributes to development of unconventional remediation strategies combining microbial degradation with subsequent UV treatment.
Item Open Access Contaminant Interactions and Biological Effects of Single-walled Carbon Nanotubes in a Benthic Estuarine System(2013) Parks, AshleySingle-walled carbon nanotubes (SWNT) are highly ordered filamentous nanocarbon structures. As their commercial and industrial use becomes more widespread, it is anticipated that SWNT will enter the environment through waste streams and product degradation. Because of their highly hydrophobic nature, SWNT aggregate and settle out of aqueous environments, especially in saline environments such as estuaries. Therefore, sediments are a likely environmental sink for SWNT once released. It is important to understand how these materials will impact benthic estuarine systems since they are the probable target area for SWNT exposure in addition to containing many lower trophic level organisms whose survvial and contaminant body burdens can have a large impact on the overall ecosystem. Disruptions in lower trophic level organism survival can have negative consequences for higher trophic levels, impacting the overall health of the ecosystem. It is also important to consider contaminant bioaccumulation, trophic transfer and biomagnification. If SWNT are taken up by benthic invertebrates, there is the possibility for trophic transfer, increasing the exposure of SWNT to higher trophic level organisms that otherwise would not have been exposed. If this type of transfer occurs in environmentally important species, the potential for human exposure may increase. My research aims to determine the magnitude of the toxicity and bioaccumulation of SWNT in benthic estuarine systems, as well as determine how they interact with other contaminants in the environment. This research will contribute to the knowledge base necessary for performing environmental risk assessments by providing information on the effects of SWNT to benthic estuarine systems.
Before investigating the environmental effects of SWNT, it is imperative that a measurement method is established to detect and quantify SWNT once they enter the environment. This research utilized pristine, semiconducting SWNT to develop extraction and measurement methods to detect and quantify these specific materials in environmental media using near infrared fluorescence (NIRF) spectroscopy. Semiconducting SWNT fluoresce in the near infrared (NIR) spectrum when excited with visible&ndashNIR light. This unique optical property can be used to selectively measure SWNT in complex media.
The fate, bioavailability, bioaccumulation and toxicity of SWNT have not been extensively studied to date. Pristine SWNT are highly hydrophobic and have been shown to strongly associate with natural particulate matter in aquatic environments. In light of this, I have focused my research to examine the influence of sediment and food exposure routes on bioavailability, bioaccumulation, and toxicity of structurally diverse SWNT in several ecologically-important marine invertebrate species. No significant mortality was observed in any organism at concentrations up to 1000 mg/kg. Evidence of biouptake after ingestion was observed for pristine semiconducting SWNT using NIRF spectroscopy and for oxidized 14C&ndashSWNT using liquid scintillation counting. After a 24 hour depuration period, the pristine semiconducting SWNT were eliminated from organisms to below the method detection limit (5 &mug/mL), and the 14C&ndashSWNT body burden was decreased by an order of magnitude to a bioaccumulation factor (BAF) of <0.01. Neither pristine SWNT nor oxidized 14C&ndashSWNT caused environmentally relevant toxicity or bioaccumulation in benthic invertebrates. Overall, the SWNT were not bioavailable and appear to associate with the sediment.
In addition to investigating the toxicity and bioaccumulation of SWNT as an independent toxicant, it is important to consider how they will interact with other contaminants in the environment (i.e., increase or decrease toxicity and bioaccumulation of co&ndashcontaminants, alter the environmental transport of co&ndashcontaminants, induce degradation of co&ndashcontaminants, etc.). I wanted to investigate the effects of SWNT on a complex mixture of contaminants already present in a natural system. New Bedford Harbor (NBH) sediment, which is contaminated with polychlorinated biphenyls (PCBs), was amended with pristine SWNT to determine if the presence of SWNT would mitigate the toxicity and bioaccumulation of the PCBs in deposit-feeding invertebrates. A dilution series of the NBH sediment was created using uncontaminated Long Island Sound (LIS) sediment to test 25% NBH sediment, 50% NBH sediment, 75% NBH sediment, and 100% NBH sediment. The results of this work showed increased organism survival and decreased bioaccumulation of PCBs in treatments amended with SWNT, with the greatest reduction observed in the 25% NBH sediment treatment group amended with 10 mg SWNT/g dry sediment. Polyethylene (PE) passive samplers indicated a reduction of interstitial water (ITW) PCB concentration of greater than 90% in the 25% NBH sediment + 10 mg SWNT/g dry sediment amendment. The ITW concentration was reduced because PCBs were not desorbing from the SWNT. Lower bioavailability leads to reduced potential for toxic effects, supporting the observation of increased survival and decreased bioaccumulation. Once in the sediment, not only are SWNT not bioavailable, they act as a highly sorptive phase, such as black carbon (BC), into which hydrophobic organic contaminants (HOCs), such as PCBS and polycyclic aromatic hydrocarbons (PAHs), can partition, thereby reducing the toxicity and bioavailability of co-occurring HOCs.
To more fully understand the impact of SWNT in this environment, their biodegradability also needs to be investigated. Biodegradation of SWNT could lead to release and/or transformation of sorbed HOCs as well as a change in the inherent transport, toxicity, and bioaccumulation of SWNT in the estuarine environment. Because the persistence of SWNT will be a primary determinant of the fate of these materials in the environment, I conducted experiments to determine if the fungus Trametes versicolor, the natural bacterial communities present in NBH sediment, and municipal wastewater treatment plant sludge could degrade or mineralize oxidized 14C&ndashSWNT. Over a six month time period, no significant degradation or mineralization was observed. In all treatments, approximately 99% of the 14C-SWNT remained associated with the solid phase, with only approximately 0.8% of added 14C present as dissolved species and only 0.1% present as 14CO2. These small pools of non-SWNT 14C were likely due to trace impurities, as no differences in production were observed between treatments and abiotic (killed) controls.