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- Genre: Academic theses
Description
The microorganisms that colonize the gastrointestinal tract have been recognized over the last several decades to have a significant bearing on the health trajectories of the hosts that harbor them. The collection of these gut microbes display links with acute and chronic disease, garnering substantial interest in leveraging the microbiome for improved health states. How these microbes assemble as a complex community and interact with each other, and the host depends on a multitude of factors. In adulthood, diet is one of the main moderators, having a significant influence on community composition and the functional output captured in the metabolites produced and/or modified by the gut microbiome. Thus, the assembly of microbes in the gut are tightly intertwined with health. In this dissertation, I examine the impact of diet and feeding behaviors on the gut microbiome and what features may be grounding or responsive under such pressures. Specifically, I first explore the avian gut microbiome as a barometer of nutritional and environmental influence on host health. Birds have continually displayed robust physiology under dietary pressures, placing them in an important, though underutilized, position within the translational science framework. Second, I describe the association of food insecurity on gut microbiome and metabolome profiles in a diverse college-based sample. Food insecurity provides its own set of unique pressures, such as unintentional calorie restriction, and inconsistent dietary intake and access to healthy food options. Third, I examine the effect of a one vs. two-consecutive days of intermittent fasting on the gut microbiome, the plasma metabolome, and associated clinical outcomes in overweight and obese adults. Growing in scientific and lay popularity, dietary fasting has been noted to induce changes in the diversity of gut microflora and gut motility, though different fasting lengths have not been assessed in the context of the human microbiome. Overall, this collection of work underscores that the community of microbes in the gut are individualized, resilient, and baseline composition and functioning are germane to how an individual may react to a particular dietary intervention.
ContributorsMohr, Alex (Author) / Sweazea, Karen L. (Thesis advisor) / Johnston, Carol S. (Committee member) / Sears, Dorothy D. (Committee member) / Whisner, Corrie M. (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Arizona State University (Publisher)
Created2022
Description
Trichloroethene (TCE) and hexavalent chromium (Cr (VI)) are ubiquitous subsurface contaminants affecting the water quality and threatening human health. Microorganisms capable of TCE and Cr (VI) reductions can be explored for bioremediation at contaminated sites. The goal of my dissertation research was to address challenges that decrease the efficiency of bioremediation in the subsurface. Specifically, I investigated strategies to (i) promote improve microbial reductive dechlorination extent through the addition of Fe0 and (ii) Cr (VI) bio-reduction through enrichment of specialized microbial consortia. Fe0 can enhance microbial TCE reduction by inducing anoxic conditions and generating H2 (electron donor). I first evaluated the effect of Fe0 on microbial reduction of TCE (with ClO4– as co-contaminant) using semi-batch soil microcosms. Results showed that high concentration of Fe0 expected during in situ remediation inhibited microbial TCE and ClO4– reduction when added together with Dehalococcoides mccartyi-containing cultures. A low concentration of aged Fe0 enhanced microbial TCE dechlorination to ethene and supported complete microbial ClO4– reduction. I then evaluated a decoupled Fe0 and biostimulation/bioaugmentation treatment approach using soil packed columns with continuous flow of groundwater. I demonstrated that microbial TCE reductive dechlorination to ethene can be benefitted by Fe0 abiotic reactions, when biostimulation and bioaugmentation are performed downstream of Fe0 addition. Furthermore, I showed that ethene production can be sustained in the presence of aerobic groundwater (after Fe0 exhaustion) by the addition of organic substrates. I hypothesized that some lessons learned from TCE Bioremediation can be applied also for other pollutants that can benefit from anaerobic reductions, like Cr (VI). Bioremediation of Cr (VI) has historically relied on biostimulation of native microbial communities, partially due to the lack of knowledge of the benefits of adding enriched consortia of specialized microorganisms (bioaugmentation). To determine the merits of a specialized consortium on bio-reduction of Cr (VI), I first enriched a culture on lactate and Cr (VI). The culture had high abundance of putative Morganella species and showed rapid and sustained Cr (VI) bio-reduction compared to a subculture grown with lactate only (without Morganella). Overall, this dissertation work documents possible strategies for synergistic abiotic and biotic chlorinated ethenes reduction, and highlights that specialized consortia may benefit Cr (VI) bio-reduction.
ContributorsMohana Rangan, Srivatsan (Author) / Krajmalnik-Brown, Rosa (Thesis advisor) / Delgado, Anca G (Thesis advisor) / Torres, César I (Committee member) / van Paassen, Leon (Committee member) / Arizona State University (Publisher)
Created2022
Description
While most household surfactants are biodegradable in aerobic conditions, their presence in a microbiological treatment process can lead to the proliferation of antimicrobial-resistance genes (ARG) in bacteria, such as Pseudomonas aeruginosa. Surfactants can be cationic, anionic, or zwitterionic, and these different classes may have different effects on the proliferation of ARG. This study evaluated how the three classes of surfactants affected the microbial community’s structure and ARG in O2-based membrane biofilm reactors (O2-MBfRs) that provided at least 98% surfactant removal. Cationic cetrimonium bromide (CTAB) had by far the strongest impact with highest ARG abundance in the biofilm. In particular, Pseudomonas and Stenotrophomonas, the two main genera in the biofilm treating CTAB, were highly correlated to the abundance of ARG for efflux pumps and antibiotic inactivation. CTAB also promoted potential of horizontal gene transfer (HGT) of ARG. Combining results from the metabolome and metagenome identified four possible pathways for CTAB biodegradation. Of special important is a new pathway: β-carbon oxidation of CTAB to produce betaine. An insufficient nitrogen source could lead to irreversible ARB and ARG enrichment in the MBfR biofilm. Finally, a two-stage O2-MBfR successfully removed a high concentration (730 mg/L) of CTAB: Partial CTAB removal in the Lead reactor relieved inhibition in the Lag reactor. Metagenomic analysis also revealed that the Lag reactor was enriched in genes for CTAB and metabolite oxygenation.
ContributorsZheng, Chenwei (Author) / Rittmann, Bruce (Thesis advisor) / Delgado, Anca (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Lai, Yen-Jung (Committee member) / Arizona State University (Publisher)
Created2023
Description
Under current climate conditions northern peatlands mostly act as C sinks; however, changes in climate and environmental conditions, can change the soil carbon decomposition cascade, thus altering the sink status. Here I studied one of the most abundant northern peatland types, poor fen, situated along a climate gradient from tundra (Daring Lake, Canada) to boreal forest (Lutose, Canada) to temperate broadleaf and mixed forest (Bog Lake, MN and Chicago Bog, NY) biomes to assess patterns of microbial abundance across the climate gradient. Principal component regression analysis of the microbial community and environmental variables determined that mean annual temperature (MAT) (r2=0.85), mean annual precipitation (MAP) (r2=0.88), and soil temperature (r2=0.77), were the top significant drivers of microbial community composition (p < 0.001). Niche breadth analysis revealed the relative abundance of Intrasporangiaceae, Methanobacteriaceae and Candidatus Methanoflorentaceae fam. nov. to increase when MAT and MAP decrease. The same analysis showed Spirochaetaceae, Methanosaetaceae and Methanoregulaceae to increase in relative abundance when MAP, soil temperature and MAT increased, respectively. These findings indicated that climate variables were the strongest predictors of microbial community composition and that certain taxa, especially methanogenic families demonstrate distinct patterns across the climate gradient. To evaluate microbial production of methanogenic substrates, I carried out High Resolution-DNA-Stable Isotope Probing (HR-DNA-SIP) to evaluate the active portion of the community’s intermediary ecosystem metabolic processes. HR-DNA-SIP revealed several challenges in efficiency of labelling and statistical identification of responders, however families like Veillonellaceae, Magnetospirillaceae, Acidobacteriaceae 1, were found ubiquitously active in glucose amended incubations. Differences in metabolic byproducts from glucose amendments show distinct patterns in acetate and propionate accumulation across sites. Families like Spirochaetaceae and Sphingomonadaceae were only found to be active in select sites of propionate amended incubations. By-product analysis from propionate incubations indicate that the northernmost sites were acetate-accumulating communities.
These results indicate that microbial communities found in poor fen northern peatlands are strongly influenced by climate variables predicted to change under current climate scenarios. I have identified patterns of relative abundance and activity of select microbial taxa, indicating the potential for climate variables to influence the metabolic pathway in which carbon moves through peatland systems.
ContributorsSarno, Analissa Flores (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Childers, Daniel (Committee member) / Arizona State University (Publisher)
Created2022
Description
This study investigated the difference in biofilm growth on pristine and aged polypropylene microplastics exposed to Tempe Town Lake water for 8 weeks. The research question here is, does the aging of microplastic (MPs) change the biofilm formation rate and composition of the biofilm in comparison with the pristine MPs. To answer this question, the biofilm formation was quantified using different methods over time for both pristine polypropylene and aged polypropylene using agar plate counts and crystal violet staining. Colony counts based on agar plating showed an increase in microbial growth over the 8 weeks of treatment, with the aged MPs accumulating higher microbial counts than the pristine MPs. The diversity of the biofilm decreased over time for both MPs and the aged MPs had overall less diversity in biofilm, based on phenotype enumeration, in comparison with the pristine MPs. Higher biofilm growth on aged MPs was confirmed using crystal violet staining, which stains the negatively charged biological compounds such as proteins and the extracellular polymeric substance matrix of the biofilm. Using this complementary approach to colony counting, the same trend of higher biofilm growth on aged MPs was found. Further studies will focus on confirming the phenotype findings using microbiome analysis following DNA extraction. This project created a methodology to quantify biofilm formation on MPs, which was used to show that MPs may accumulate more biofilms in the environment as they age under sunlight.
ContributorsMushro, Noelle (Author) / Perreault, Francois (Thesis advisor) / Hamilton, Kerry (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Arizona State University (Publisher)
Created2022
Characterization and Manipulation of Microbiomes From Arid Landfills for Improved Methane Production
Description
Environmentally harmful byproducts from solid waste’s decomposition, including methane (CH4) emissions, are managed through standardized landfill engineering and gas-capture mechanisms. Yet only a limited number of studies have analyzed the development and composition of Bacteria and Archaea involved in CH4 production from landfills. The objectives of this research were to compare microbiomes and bioactivity from CH4-producing communities in contrasting spatial areas of arid landfills and to tests a new technology to biostimulate CH4 production (methanogenesis) from solid waste under dynamic environmental conditions controlled in the laboratory. My hypothesis was that the diversity and abundance of methanogenic Archaea in municipal solid waste (MSW), or its leachate, play an important role on CH4 production partially attributed to the group’s wide hydrogen (H2) consumption capabilities. I tested this hypothesis by conducting complementary field observations and laboratory experiments. I describe niches of methanogenic Archaea in MSW leachate across defined areas within a single landfill, while demonstrating functional H2-dependent activity. To alleviate limited H2 bioavailability encountered in-situ, I present biostimulant feasibility and proof-of-concepts studies through the amendment of zero valent metals (ZVMs). My results demonstrate that older-aged MSW was minimally biostimulated for greater CH4 production relative to a control when exposed to iron (Fe0) or manganese (Mn0), due to highly discernable traits of soluble carbon, nitrogen, and unidentified fluorophores found in water extracts between young and old aged, starting MSW. Acetate and inhibitory H2 partial pressures accumulated in microcosms containing old-aged MSW. In a final experiment, repeated amendments of ZVMs to MSW in a 600 day mesocosm experiment mediated significantly higher CH4 concentrations and yields during the first of three ZVM injections. Fe0 and Mn0 experimental treatments at mesocosm-scale also highlighted accelerated development of seemingly important, but elusive Archaea including Methanobacteriaceae, a methane-producing family that is found in diverse environments. Also, prokaryotic classes including Candidatus Bathyarchaeota, an uncultured group commonly found in carbon-rich ecosystems, and Clostridia; All three taxa I identified as highly predictive in the time-dependent progression of MSW decomposition. Altogether, my experiments demonstrate the importance of H2 bioavailability on CH4 production and the consistent development of Methanobacteriaceae in productive MSW microbiomes.
ContributorsReynolds, Mark Christian (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Krajmalnik-Brown, Rosa (Thesis advisor) / Wang, Xuan (Committee member) / Kavazanjian, Edward (Committee member) / Arizona State University (Publisher)
Created2022
Description
Electroactive bacteria connect biology to electricity, acting as livingelectrochemical catalysts. In nature, these bacteria can respire insoluble compounds like
iron oxides, and in the laboratory, they are able to respire an electrode and produce an
electrical current. This document investigates two of these electroactive bacteria:
Geobacter sulfurreducens and Thermincola ferriacetica. G. sulfurreducens is a Gramnegative iron-reducing soil bacterium, and T. ferriacetica is a thermophilic, Grampositive bacterium that can reduce iron minerals and several other electron acceptors.
Respiring insoluble electron acceptors like metal oxides presents challenges to a
bacterium. The organism must extend its electron transport chain from the inner
membrane outside the cell and across a significant distance to the surface of the electron
acceptor. G. sulfurreducens is one of the most-studied electroactive bacteria, and despite
this there are many gaps in knowledge about its mechanisms for transporting electrons
extracellularly. Research in this area is complicated by the presence of multiple pathways
that may be concurrently expressed. I used cyclic voltammetry to determine which
pathways are present in electroactive biofilms of G. sulfurreducens grown under different
conditions and correlated this information with gene expression data from the same
conditions. This correlation presented several genes that may be components of specific
pathways not just at the inner membrane but along the entire respiratory pathway, and I
propose an updated model of the pathways in this organism. I also characterized the
composition of G. sulfurreducens and found that it has high iron and lipid content
independent of growth condition, and the high iron content is explained by the large
abundance of multiheme cytochrome expression that I observed. I used multiple
microscopy techniques to examine extracellular respiration in G. sulfurreducens, and in
the process discovered a novel organelle: the intracytoplasmic membrane. I show 3D
reconstructions of the organelle in G. sulfurreducens and discuss its implications for the
cell’s metabolism. Finally, I discuss gene expression in T. ferriacetica in RNA samples
collected from an anode-respiring culture and highlight the most abundantly expressed
genes related to anode-respiring metabolism.
ContributorsHowley, Ethan Thomas (Author) / Torres, César I (Thesis advisor) / Krajmalnik-Brown, Rosa (Thesis advisor) / Nannenga, Brent (Committee member) / Arizona State University (Publisher)
Created2022
Description
Bioremediation of trichloroethene (TCE) using Dehalococcoides mccartyi-containing microbial cultures is a recognized and successful remediation technology. Our work with an upflow anaerobic sludge blanket (UASB) reactor has shown that high-performance, fast-rate dechlorination of TCE can be achieved by promoting bioflocculation of Dehalococcoides mccartyi-containing cultures. The bioreactor achieved high maximum conversion rates of 1.63 ± 0.012 mmol Cl- Lculture-1 h-1 at an HRT of 3.6 hours and >97% dechlorination of TCE to ethene while continuously fed 2 mM TCE. The UASB generated bioflocs from a microbially heterogeneous dechlorinating culture and produced Dehalococcoides mccartyi densities of 1.73x10-13 cells Lculture-1 indicating that bioflocculation of Dehalococcoides mccartyi-containing cultures can lead to high density inocula and high-performance, fast-rate bioaugmentation culture for in situ treatment. The successful operation of our pilot scale bioreactor led to the assessment of the technology as an onsite ex-situ treatment system. The bioreactor was then fed TCE-contaminated groundwater from the Motorola Inc. 52nd Street Plant Superfund site in Phoenix, AZ augmented with the lactate and methanol. The bioreactor maintained >99% dechlorination of TCE to ethene during continuous operation at an HRT of 3.2 hours. Microbial community analysis under both experimental conditions reveals shifts in the community structure although maintaining high rate dechlorination. High density dechlorinating cultures containing bioflocs can provide new ways to 1) produce dense bioaugmentation cultures, 2) perform ex-situ bioremediation of TCE, and 3) increase our understanding of Dehalococcoides mccartyi critical microbial interactions that can be exploited at contaminated sites in order to improve long-term bioremediation schemes.
ContributorsFajardo-Williams, Devyn (Author) / Krajmalnik-Brown, Rosa (Thesis advisor) / Torres, César I (Committee member) / Popat, Sudeep C (Committee member) / Arizona State University (Publisher)
Created2015
Description
Microbial Electrochemical Cell (MXC) technology harnesses the power stored in wastewater by using anode respiring bacteria (ARB) as a biofilm catalyst to convert the energy stored in waste into hydrogen or electricity. ARB, or exoelectrogens, are able to convert the chemical energy stored in wastes into electrical energy by transporting electrons extracellularly and then transferring them to an electrode. If MXC technology is to be feasible for ‘real world’ applications, it is essential that diverse ARB are discovered and their unique physiologies elucidated- ones which are capable of consuming a broad spectrum of wastes from different contaminated water sources.
This dissertation examines the use of Gram-positive thermophilic (60 ◦C) ARB in MXCs since very little is known regarding the behavior of these microorganisms in this setting. Here, we begin with the draft sequence of the Thermincola ferriacetica genome and reveal the presence of 35 multiheme c-type cytochromes. In addition, we employ electrochemical techniques including cyclic voltammetry (CV) and chronoamperometry (CA) to gain insight into the presence of multiple pathways for extracellular electron transport (EET) and current production (j) limitations in T. ferriacetica biofilms.
Next, Thermoanaerobacter pseudethanolicus, a fermentative ARB, is investigated for its ability to ferment pentose and hexose sugars prior to using its fermentation products, including acetate and lactate, for current production in an MXC. Using CA, current production is tracked over time with the generation and consumption of fermentation products. Using CV, the midpoint potential (EKA) of the T. pseudethanolicus EET pathway is revealed.
Lastly, a cellulolytic microbial consortium was employed for the purpose ofassessing the feasibility of using thermophilic MXCs for the conversion of solid waste into current production. Here, a highly enriched consortium of bacteria, predominately from the Firmicutes phylum, is capable of generating current from solid cellulosic materials.
This dissertation examines the use of Gram-positive thermophilic (60 ◦C) ARB in MXCs since very little is known regarding the behavior of these microorganisms in this setting. Here, we begin with the draft sequence of the Thermincola ferriacetica genome and reveal the presence of 35 multiheme c-type cytochromes. In addition, we employ electrochemical techniques including cyclic voltammetry (CV) and chronoamperometry (CA) to gain insight into the presence of multiple pathways for extracellular electron transport (EET) and current production (j) limitations in T. ferriacetica biofilms.
Next, Thermoanaerobacter pseudethanolicus, a fermentative ARB, is investigated for its ability to ferment pentose and hexose sugars prior to using its fermentation products, including acetate and lactate, for current production in an MXC. Using CA, current production is tracked over time with the generation and consumption of fermentation products. Using CV, the midpoint potential (EKA) of the T. pseudethanolicus EET pathway is revealed.
Lastly, a cellulolytic microbial consortium was employed for the purpose ofassessing the feasibility of using thermophilic MXCs for the conversion of solid waste into current production. Here, a highly enriched consortium of bacteria, predominately from the Firmicutes phylum, is capable of generating current from solid cellulosic materials.
ContributorsLusk, Bradley (Author) / Torres, César I (Thesis advisor) / Rittmann, Bruce E. (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Arizona State University (Publisher)
Created2015
Description
Electro-Selective Fermentation (ESF) combines Selective Fermentation (SF) and a Microbial Electrolysis Cell (MEC) to selectively degrade carbohydrate and protein in lipid-rich microalgae biomass, enhancing lipid wet-extraction. In addition, saturated long-chain fatty acids (LCFAs) are produced via β-oxidation. This dissertation builds understanding of the biochemical phenomena and microbial interactions occurring among fermenters, lipid biohydrogenaters, and anode respiring bacteria (ARB) in ESF. The work begins by proving that ESF is effective in enhancing lipid wet-extraction from Scenedesmus acutus biomass, while also achieving “biohydrogenation” to produce saturated LCFAs. Increasing anode respiration effectively scavenges short chain fatty acids (SCFAs) generated by fermentation, reducing electron loss. However, the effectiveness of ESF depends on biochemical characteristics of the feeding biomass (FB). Four different FB batches yield different lipid-extraction performances, based on the composition of FB’s cellular structure. Finally, starting an ESF reactor with a long solid retention time (SRT), but then switching it to a short SRT provides high lipid extractability and volumetric production with low lipid los. Lipid fermenters can be flushed out with short a SRT, but starting with a short SRT fails achieve good results because fermenters needed to degrading algal protective layers also are flushed out and fail to recover when a long SRT is imposed. These results point to a potentially useful technology to harvest lipid from microalgae, as well as insight about how this technology can be best managed.
ContributorsLiu, Yuanzhen (Author) / Rittmann, Bruce E. (Thesis advisor) / Torres, César I (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Arizona State University (Publisher)
Created2019