Theses and Dissertations from UMD

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New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a give thesis/dissertation in DRUM

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    Utilizing algal turf scrubbers for bioremediation and bioenergy production
    (2023) Delp, Danielle Marie; Lansing, Stephanie A; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    This dissertation researched the conversion of algal biomass that was generated as a byproduct of bioremediation by algal turf scrubbers (ATS) into bioenergy via anaerobic digestion. Anaerobic digestion is a bacterial process that converts organic material into bioenergy in the form of biogas that contains methane (CH4), the primary component of natural gas. Bioenergy yield was quantified as the volume of CH4 generated from digestion of the algae in relation to seasonal changes in algal biomass yield, different digester operational parameters, co-digestion of the biomass with more conventional digestion feedstock, and flocculation pre-treatment for dewatering of algae prior to digestion. The first study used a pilot-scale mesophilic digester at the Port of Baltimore (Baltimore, MD, USA) to continuously digest algae from a 122 m2 ATS on the Patapsco River over two years. Biomass generation was significantly correlated to maximum daily air temperature, water temperature, and flow rate in Year 1 but only water flow rate in Year 2. Algae of the taxa Ochrophyta dominated the algal turf, especially the filamentous diatom Melosira sp., in both years. In Year 1 of the study, two anaerobic digestion systems with variable hydraulic retention times (HRT), designated D1 (average HRT 45.0 ± 5.8 days) and D2-D3 (average HRT 61.0 ± 8.1 days) were used to digest the algae. The D1 generated 1090 L CH4 from 2416 L of algae over a 39-day HRT (59.1 ± 8.9 L algae/kg VS), and D2-D3 generated 1170 L CH4 from 2337 L of algae over a 53-day HRT (67.9 ± 11.0 L algae/kg VS). The difference in CH4 yield with two different HRTs was not significant. In Year 2, only the D2-D3 was operated and was modified to test the use of active recirculation and heating to improve digestion efficiency and CH4 yield. The D2-D3 system generated 4000 L of CH4 (163 ± 42 L algae/kg VS) from 3310 L of algae in Year 2. The second study consisted of laboratory-scale biomethane potential tests to test changes in CH4 yield when algae harvested from an Anacostia River (Bladensburg, MD, USA) ATS was co-digested with three wastes (dairy manure, food waste, and poultry litter) at algae:waste loading ratios of at 1:1, 1:2, 1:5, and 1:10 by organic material, or volatile solids (VS), content. The algal biomass was the least efficient substrate at generating CH4 when normalized by both mass VS digested (109 ± 4 mL CH4/g VS) and total mass of substrate digested (0.687 ± 0.025 mL CH4/g substrate). Co-digestion with all three of the wastes at all ratios tested significantly increased CH4 generation efficiency per mass VS compared to only digesting algae. However, the high moisture content of the algae (95.2%) relative to the other co-digestion wastes (29.0-84.6%) significantly decreased CH4 production on a mass basis for the dairy manure, food waste, and poultry litter when algae was added at any loading ratio. A lettuce growth experiment using the effluent of the digestion vessels showed no signs of acute toxicity when any of the diluted (8-fold) digester effluents were applied as fertilizer to the developing plants. The third and final study consisted of flocculation experiments that tested 500-mL of algae using four experimental treatments (FeCl3, electrocoagulation, chitosan, and Bacillus sp. RP 1137) to dewater algae harvested from the Anacostia River ATS and compared to gravity settling as a control. The experimental flocculants successfully increased the total solids (TS) of the ATS algae by 14-291% depending on the treatment, with electrocoagulation being the least effective and bacterial flocculation being the most effective flocculant. All treatments reduced total suspended solids (TSS) in the drained supernatant by >98%. The raw ATS algae and dewatered solids from the settling experiment were then digested for 35-days, with the algae yielding 49.6 ± 3.6 mL of CH4/g VS. The dewatered solids had reduced digestion efficiency by 29.6-71.0% compared to untreated algae. Dewatering pre-treatment increased CH4 yield from the algae when normalized by total g substrate fed to the reactor (1.65 ± 0.12 mL CH4/g substrate) for all treatments except bacteria 1x, however the effect was only significant for solids dewatered with electrocoagulation. The results from the three studies show that temperature drives algal growth patterns in temperate climates, which results in seasonally variable biomass yield from ATS, with a corresponding variability in CH4 production due to inconsistent availability of the algal feedstock. Algae can be co-digested with agricultural and food wastes that are generated year-round to reduce variability in feedstock availability. Thickening and dewatering the algae improves CH4 yield on a mass basis, however the digestion efficiency was reduced. In conclusion, the findings suggest that anaerobic digestion is a viable means of managing the algae harvested from ATS systems with and without co-digestion of the algal biomass.
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    LEAF-ASSOCIATED PERIPHYTON IN HETEROTROPHIC STREAMS: EFFECT ON MACROINVERTEBRATE ASSEMBLAGES AND GROWTH
    (2020) Eckert, Rebecca A; Lamp, William O; Entomology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Temperate headwater streams are often shaded, limiting autochthonous production, and therefore energetically supported by allochthonous material, e.g., leaves, via fungal and bacterial decomposition. Macroinvertebrate shredders feed on this leaf matrix, providing food for other organisms. Recent work indicates that periphyton (e.g., diatoms, green algae, cyanobacteria; hereafter, algae) interacts with microbial decomposers and provides higher quality food. Little work has, however, examined these interactions in natural settings. I investigated leaf-associated algae’s impact on macroinvertebrate leaf colonization in the field, followed by measuring growth and food preferences in the lab based on field results. First, I manipulated leaf light availability in high- and low-nutrient streams in winter and spring. Leaf-associated algal and fungal biomass were positively correlated in winter. Leaf C:N negatively correlated to algae in winter and fungi in spring, while N:P and C:P negatively correlated to fungi in winter and algae in spring. These factors predicted functional feeding guild biomass and abundance, e.g., predator biomass by algal and fungal biomass and spring shredder biomass by leaf stoichiometry. Algal biomass elicited differential taxon responses; e.g., Ephemerella (Ephemeroptera:Ephemerellidae) and Stenonema (Ephemeroptera:Heptageniidae) responded positively while Tipula (Diptera:Tipulidae) responded negatively. Second, I fed light- and dark-conditioned leaves to Ephemerella invaria and Caecidotea communis (Isopoda:Asellidae), which both consumed leaves and algae. C. communis experienced greater growth on light-conditioned leaves, indicating a high-quality resource, while E. invaria had no growth differences between treatments. Third, light- and dark-conditioned leaves were offered to five taxa, Amphinemura (Plecoptera:Nemouridae), Tipula, Stenonema, Lepidostoma (Trichoptera:Lepidostomatidae), and Caecidotea communis. Tipula alone demonstrated a preference which was for dark-conditioned leaves. These results indicate that leaf-associated algae are a food resource and attractant for some macroinvertebrates and a deterrent to others. Natural headwater streams are heterogeneous with leaves exposed to varying light levels, altering leaf-associated algae and providing differential food resources. Anthropogenic impacts often homogenize these streams. Although restoration seeks to restore heterogeneity, headwater stream algae are largely ignored. This work demonstrates the important role algae play in macroinvertebrate interactions with senescent leaves, highlighting the need to incorporate allochthonous and autochthonous resources into stream restoration and management efforts to support biodiversity.
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    THE PHYTOHORMONE ETHYLENE: (I) INVESTIGATING THE MOLECULAR FUNCTION OF RTE1 AND (II) INSIGHTS ON THE EVOLUTION OF THE ETHYLENE BIOSYNTHESIS AND SIGNALING PATHWAYS
    (2017) Clay, John; Chang, Caren; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Ethylene is an important phytohormone that regulates growth, development and stress responses in land plants and charophycean green algae. In Arabidopsis thaliana, ethylene is perceived by a family of five receptors. One of these five receptors, ETR1, is dependent on REVERSION-TO-ETHYLENE1 (RTE1) and Cytochrome B5 (Cb5) while the other four receptors are not. We found that RTE1 and Cb5 interact in planta and used genetic analyses to place Cb5 upstream of RTE1 in the ethylene signaling pathway. After comparing different ethylene receptors we identified an N-terminally localized proline that is important in determining whether a receptor is RTE1-dependent. Our results suggest that Cb5 receives electrons from upstream redox molecules, passes these electrons to RTE1; RTE1 is then able to activate the ETR1 receptor possibly by acting a molecular chaperone that refolds the ETR1 receptor into an active conformation. The ethylene signal transduction pathway is functionally conserved in the charophycean green algae such as Spirogyra pratensis, suggesting that this signaling pathway was present in the common ancestor of charophytes and land plants over 450 million years ago. However, it is unclear whether the central regulator of ethylene response, EIN2, was conserved in charophytes. Furthermore, the details of ethylene biosynthesis in charophytes were unresolved. After examining the genomes and transcriptomes of many green algae we are able to report that EIN2 is conserved in most charophytes and even some of the more distantly related chlorophycean green algae. Moreover, the Spirogyra EIN2 is functionally conserved and able to activate ethylene responses in Arabidopsis. Ethylene is synthesized via a two-step reaction involving the conversion of S-adenosyl-L-methionine (SAM) to 1-aminocyclopropane-1-carboxylic acid (ACC) by the enzyme ACC synthase (ACS), followed by oxidation of ACC to ethylene gas by the enzyme ACC oxidase (ACO). We identified S. pratensis ACS homologs and demonstrated that S. pratensis can synthesize ACC. S. pratensis lacks ACO homologs but we find it is still capable of producing low levels of ethylene. From our results we conclude that the ethylene biosynthesis and signaling pathways were established in early charophytes allowing these algae to establish ethylene as an important signalling molecule.
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    Dinoflagellate Genomic Organization and Phylogenetic Marker Discovery Utilizing Deep Sequencing Data
    (2016) Mendez, Gregory Scott; Delwiche, Charles F; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Dinoflagellates possess large genomes in which most genes are present in many copies. This has made studies of their genomic organization and phylogenetics challenging. Recent advances in sequencing technology have made deep sequencing of dinoflagellate transcriptomes feasible. This dissertation investigates the genomic organization of dinoflagellates to better understand the challenges of assembling dinoflagellate transcriptomic and genomic data from short read sequencing methods, and develops new techniques that utilize deep sequencing data to identify orthologous genes across a diverse set of taxa. To better understand the genomic organization of dinoflagellates, a genomic cosmid clone of the tandemly repeated gene Alchohol Dehydrogenase (AHD) was sequenced and analyzed. The organization of this clone was found to be counter to prevailing hypotheses of genomic organization in dinoflagellates. Further, a new non-canonical splicing motif was described that could greatly improve the automated modeling and annotation of genomic data. A custom phylogenetic marker discovery pipeline, incorporating methods that leverage the statistical power of large data sets was written. A case study on Stramenopiles was undertaken to test the utility in resolving relationships between known groups as well as the phylogenetic affinity of seven unknown taxa. The pipeline generated a set of 373 genes useful as phylogenetic markers that successfully resolved relationships among the major groups of Stramenopiles, and placed all unknown taxa on the tree with strong bootstrap support. This pipeline was then used to discover 668 genes useful as phylogenetic markers in dinoflagellates. Phylogenetic analysis of 58 dinoflagellates, using this set of markers, produced a phylogeny with good support of all branches. The Suessiales were found to be sister to the Peridinales. The Prorocentrales formed a monophyletic group with the Dinophysiales that was sister to the Gonyaulacales. The Gymnodinales was found to be paraphyletic, forming three monophyletic groups. While this pipeline was used to find phylogenetic markers, it will likely also be useful for finding orthologs of interest for other purposes, for the discovery of horizontally transferred genes, and for the separation of sequences in metagenomic data sets.
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    Genomic studies of the evolution of haptophytes and dinoflagellates with emphasis on the chromalveolate hypothesis
    (2006-06-08) Sanchez Puerta, Maria Virginia; Delwiche, Charles F; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    All photosynthetic eukaryotes rely, partially or totally, on their plastids to live. The plastids, which ultimately are highly modified cyanobacteria, were acquired through a process of primary, secondary, or tertiary endosymbiosis. Four photosynthetic lineages, including haptophytes, dinoflagellates, cryptophytes, and heterokonts, contain secondary plastids with chlorophyll c as a main photosynthetic pigment. These four lineages were grouped together, along with their heterotrophic relatives, on the basis of their pigmentation and called chromalveolates by Cavalier-Smith. However, the phylogenetic relationships among these algae are unknown and the chromalveolate hypothesis remains very controversial. This study focuses on increasing the amount of genomic data from a poorly studied chromalveolate lineage, the haptophytes, and understanding plastid evolution in chromalveolates. Both the chloroplast and mitochondrial genomes of the haptophyte <em>Emiliania huxleyi</em> were sequenced and examined to describe basic genomic properties, as well as perform comparative studies. Phylogenetic analyses, including data acquired from haptophytes, support a monophyletic chl c containing plastid clade derived from the red algae, after the divergence of Cyanidiales, with the cryptophyte plastid basal or sister to the haptophyte plastid. In addition, phylogenetic analyses using mitochondrial data suggest a relationship of haptophytes and cryptophytes. The chromalveolate clade as a whole is not recovered nor rejected by the data. Analysis of an EST project from the heterotrophic dinoflagellate <em>Crypthecodinium cohnii</em> indicates that <em>C. cohnii</em> is not only derived from a photosynthetic ancestor, but very likely retains a non-photosynthetic plastid. Analyses of putative gene function suggest that heme biosynthesis, non-mevalonate isoprenoid biosynthesis, amino-acid metabolism, and Fe-S cluster assembly may occur in the plastid. These observations are also consistent with the chromalveolate hypothesis, which proposes that several major groups of eukaryotes, including alveolates, haptophytes, cryptophytes, and heterokonts, may form a monophyletic group with a photosynthetic common ancestor, and that nonphotosynthetic members are secondarily so.