Matching Items (48)
Description
Reductive dechlorination by members of the bacterial genus Dehalococcoides is a common and cost-effective avenue for in situ bioremediation of sites contaminated with the chlorinated solvents, trichloroethene (TCE) and perchloroethene (PCE). The overarching goal of my research was to address some of the challenges associated with bioremediation timeframes by improving the rates of reductive dechlorination and the growth of Dehalococcoides in mixed communities. Biostimulation of contaminated sites or microcosms with electron donor fails to consistently promote dechlorination of PCE/TCE beyond cis-dichloroethene (cis-DCE), even when the presence of Dehalococcoides is confirmed. Supported by data from microcosm experiments, I showed that the stalling at cis-DCE is due a H2 competition in which components of the soil or sediment serve as electron acceptors for competing microorganisms. However, once competition was minimized by providing selective enrichment techniques, I illustrated how to obtain both fast rates and high-density Dehalococcoides using three distinct enrichment cultures. Having achieved a heightened awareness of the fierce competition for electron donor, I then identified bicarbonate (HCO3-) as a potential H2 sink for reductive dechlorination. HCO3- is the natural buffer in groundwater but also the electron acceptor for hydrogenotrophic methanogens and homoacetogens, two microbial groups commonly encountered with Dehalococcoides. By testing a range of concentrations in batch experiments, I showed that methanogens are favored at low HCO3 and homoacetogens at high HCO3-. The high HCO3- concentrations increased the H2 demand which negatively affected the rates and extent of dechlorination. By applying the gained knowledge on microbial community management, I ran the first successful continuous stirred-tank reactor (CSTR) at a 3-d hydraulic retention time for cultivation of dechlorinating cultures. I demonstrated that using carefully selected conditions in a CSTR, cultivation of Dehalococcoides at short retention times is feasible, resulting in robust cultures capable of fast dechlorination. Lastly, I provide a systematic insight into the effect of high ammonia on communities involved in dechlorination of chloroethenes. This work documents the potential use of landfill leachate as a substrate for dechlorination and an increased tolerance of Dehalococcoides to high ammonia concentrations (2 g L-1 NH4+-N) without loss of the ability to dechlorinate TCE to ethene.
ContributorsDelgado, Anca Georgiana (Author) / Krajmalnik-Brown, Rosa (Thesis advisor) / Cadillo-Quiroz, Hinsby (Committee member) / Halden, Rolf U. (Committee member) / Rittmann, Bruce E. (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2013
Description
Despite the breadth of studies investigating ecosystem development, an underlying theory guiding this process remains elusive. Several principles have been proposed to explain ecosystem development, though few have garnered broad support in the literature. I used boreal wetland soils as a study system to test a notable goal oriented principle: The Maximum Power Principle (MPP). The MPP posits that ecosystems, and in fact all energy systems, develop to maximize power production or the rate of energy production. I conducted theoretical and empirical investigations to test the MPP in northern wetlands.
Permafrost degradation is leading to rapid wetland formation in northern peatland ecosystems, altering the role of these ecosystems in the global carbon cycle. I reviewed the literature on the history of the MPP theory, including tracing its origins to The Second Law of Thermodynamics. To empirically test the MPP, I collected soils along a gradient of ecosystem development and: 1) quantified the rate of adenosine triphosphate (ATP) production--literally cellular energy--to test the MPP; 2) quantified greenhouse gas production (CO2, CH4, and N2O) and microbial genes that produce enzymes catalyzing greenhouse gas production, and; 3) sequenced the 16s rRNA gene from soil microbes to investigate microbial community composition across the chronosequence of wetland development. My results suggested that the MPP and other related theoretical constructs have strong potential to further inform our understanding of ecosystem development. Soil system power (ATP) decreased temporarily as the ecosystem reorganized after disturbance to rates of power production that approached pre-disturbance levels. Rates of CH4 and N2O production were higher at the newly formed bog and microbial genes involved with greenhouse gas production were strongly related to the amount of greenhouse gas produced. DNA sequencing results showed that across the chronosequence of development, the two relatively mature ecosystems--the peatland forest ecosystem prior to permafrost degradation and the oldest bog--were more similar to one another than to the intermediate, less mature bog. Collectively, my results suggest that ecosystem age, rather than ecosystem state, was a more important driver for ecosystem structure and function.
Permafrost degradation is leading to rapid wetland formation in northern peatland ecosystems, altering the role of these ecosystems in the global carbon cycle. I reviewed the literature on the history of the MPP theory, including tracing its origins to The Second Law of Thermodynamics. To empirically test the MPP, I collected soils along a gradient of ecosystem development and: 1) quantified the rate of adenosine triphosphate (ATP) production--literally cellular energy--to test the MPP; 2) quantified greenhouse gas production (CO2, CH4, and N2O) and microbial genes that produce enzymes catalyzing greenhouse gas production, and; 3) sequenced the 16s rRNA gene from soil microbes to investigate microbial community composition across the chronosequence of wetland development. My results suggested that the MPP and other related theoretical constructs have strong potential to further inform our understanding of ecosystem development. Soil system power (ATP) decreased temporarily as the ecosystem reorganized after disturbance to rates of power production that approached pre-disturbance levels. Rates of CH4 and N2O production were higher at the newly formed bog and microbial genes involved with greenhouse gas production were strongly related to the amount of greenhouse gas produced. DNA sequencing results showed that across the chronosequence of development, the two relatively mature ecosystems--the peatland forest ecosystem prior to permafrost degradation and the oldest bog--were more similar to one another than to the intermediate, less mature bog. Collectively, my results suggest that ecosystem age, rather than ecosystem state, was a more important driver for ecosystem structure and function.
ContributorsChapman, Eric (Author) / Childers, Daniel L. (Thesis advisor) / Cadillo-Quiroz, Hinsby (Committee member) / Hall, Sharon J (Committee member) / Turetsky, Merritt (Committee member) / Arizona State University (Publisher)
Created2015
Description
Trichloroethene (TCE) is a ubiquitous soil and groundwater contaminant. The most common bioremediation approach for TCE relies on the process of reductive dechlorination by Dehalococcoides mccartyi. D. mccartyi use TCE, dichloroethene, and vinyl chloride as electron acceptors and hydrogen as an electron donor. At contaminated sites, reductive dechlorination is typically promoted by adding a fermentable substrate, which is broken down to short chain fatty acids, simple alcohols, and hydrogen. This study explored microbial chain elongation (MCE), instead of fermentation, to promote TCE reductive dechlorination. In MCE, microbes use simple substrates (e.g., acetate, ethanol) to build medium chain fatty acids and also produce hydrogen during this process. Soil microcosm using TCE and acetate and ethanol as MCE substrates were established under anaerobic conditions. In soil microcosms with synthetic groundwater and natural groundwater, ethene was the main product from TCE reductive dechlorination and butyrate and hydrogen were the main products from MCE. Transfer microcosms using TCE and either acetate and ethanol, ethanol, or acetate were also established. The transfers with TCE and ethanol showed the faster rates of reductive dechlorination and produced more elongated products (i.e., hexanoate). The microbial groups enriched in the soil microcosms likely responsible for chain elongation were most similar to Clostridium genus. These investigations showed the potential for synergistic microbial chain elongation and reductive dechlorination of chlorinated ethenes.
ContributorsRobles, Aide (Author) / Delgado, Anca G. (Thesis advisor) / Torres, Cesar I. (Committee member) / van Paassen, Leon (Committee member) / Arizona State University (Publisher)
Created2019
Description
This research explores microbial chain elongation as a pathway for production of complex organic compounds in soils with implication for the carbon cycle. In chain elongation, simple substrates such as ethanol and short chain carboxylates such as acetate can be converted to longer carbon chain carboxylates under anaerobic conditions through cyclic, reverse β oxidation. This pathway elongates the carboxylate by two carbons. The chain elongation process is overall thermodynamically feasible, and microorganisms gain energy through this process. There have been limited insights into the versatility of chain elongating substrates, understanding the chain elongating microbial community, and its importance in sequestering carbon in the soils.
We used ethanol, methanol, butanol, and hydrogen as electron donors and acetate and propionate as electron acceptors to test the occurrence of microbial chain elongation in four soils with different physicochemical properties and microbial communities. Common chain elongation products were the even numbered chains butyrate, caproate, and butanol, the odd numbered carboxylates valerate and heptanoate, along with molecular hydrogen. At a near neutral pH and mesophilic temperature, we observed a stable and sustained production of longer fatty acids along with hydrogen. Microbial community analysis show phylotypes from families such as Clostridiaceae, Bacillaceae, and Ruminococcaceae in all tested conditions. Through chain elongation, the products formed are less biodegradable. They may undergo transformations and end up as organic carbon, decreasing the greenhouse gas emissions, thus, making this process important to study.
We used ethanol, methanol, butanol, and hydrogen as electron donors and acetate and propionate as electron acceptors to test the occurrence of microbial chain elongation in four soils with different physicochemical properties and microbial communities. Common chain elongation products were the even numbered chains butyrate, caproate, and butanol, the odd numbered carboxylates valerate and heptanoate, along with molecular hydrogen. At a near neutral pH and mesophilic temperature, we observed a stable and sustained production of longer fatty acids along with hydrogen. Microbial community analysis show phylotypes from families such as Clostridiaceae, Bacillaceae, and Ruminococcaceae in all tested conditions. Through chain elongation, the products formed are less biodegradable. They may undergo transformations and end up as organic carbon, decreasing the greenhouse gas emissions, thus, making this process important to study.
ContributorsJoshi, Sayalee (Author) / Delgado, Anca G (Thesis advisor) / Torres, César I (Committee member) / van Paassen, Leon (Committee member) / Arizona State University (Publisher)
Created2018
Description
Peatlands represent 3% of the earth’s surface but have been estimated to contain up to 30% of all terrestrial soil organic carbon and release an estimated 40% of global atmospheric CH4 emissions. Contributors to the production of CH4 are methanogenic Archaea through a coupled metabolic dependency of end products released by heterotrophic bacteria within the soil in the absence of O2. To better understand how neighboring bacterial communities can influence methanogenesis, the isolation and physiological characterization of two novel isolates, one Methanoarchaeal isolate and one Acidobacterium isolate identified as QU12MR and R28S, respectively, were targeted in this present study. Co-culture growth in varying temperatures of the QU12MR isolate paired with an isolated Clostridium species labeled R32Q and the R28S isolate were also investigated for possible influences in CH4 production. Phylogenetic analysis of strain QU12MR was observed as a member of genus Methanobacterium sharing 98% identity similar to M. arcticum strain M2 and 99% identity similar to M. uliginosum strain P2St. Phylogenetic analysis of strain R28S was associated with genus Acidicapsa from the phylum Acidobacteria, sharing 97% identity to A. acidisoli strain SK-11 and 96% identity similarity to Occallatibacter savannae strain A2-1c. Bacterial co-culture growth and archaeal CH4 production was present in the five temperature ranges tested. However, bacterial growth and archaeal CH4 production was less than what was observed in pure culture analysis after 21 days of incubation.
ContributorsRamirez, Zeni Elizia (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Roberson, Robert (Thesis advisor) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2018
Description
Laterally-loaded short rigid drilled shaft foundations are the primary foundation used within the electric power transmission line industry. Performance of these laterally loaded foundations is dependent on modulus of the subsurface, which is directly measured by the Pressuremeter (PMT). The PMT test provides the lateral shear modulus at intermediate strains, an equivalent elastic modulus for lateral loading, which mimics the reaction of transmission line foundations within the elastic range of motion. The PMT test, however, is expensive to conduct and rarely performed. Correlations of PMT to blow counts and other index properties have been developed but these correlations have high variability and may result in unconservative foundation design. Variability in correlations is due, in part, because difference of the direction of the applied load and strain level between the correlated properties and the PMT. The geophysical shear wave velocity (S-wave velocity) as measured through refraction microtremor (ReMi) methods can be used as a measure of the small strain, shear modulus in the lateral direction. In theory, the intermediate strain modulus of the PMT is proportional to the small strain modulus of S-wave velocity. A correlation between intermediate strain and low strain moduli is developed here, based on geophysical surveys conducted at fourteen previous PMT testing locations throughout the Sonoran Desert of central Arizona. Additionally, seasonal variability in S-wave velocity of unsaturated soils is explored and impacts are identified for the use of the PMT correlation in transmission line foundation design.
ContributorsEvans, Ashley Elizabeth (Author) / Houston, Sandra (Thesis advisor) / Zapata, Claudia (Thesis advisor) / van Paassen, Leon (Committee member) / Arizona State University (Publisher)
Created2018
Description
Utilizing both 16S and 18S rRNA sequencing alongside energetic calculations from geochemical measurements offers a bridged perspective of prokaryotic and eukaryotic community diversities and their relationships to geochemical diversity. Yellowstone National Park hot spring outflows from varied geochemical compositions, ranging in pH from < 2 to > 9 and in temperature from < 30°C to > 90°C, were sampled across the photosynthetic fringe, a transition in these outflows from exclusively chemosynthetic microbial communities to those that include photosynthesis. Illumina sequencing was performed to document the diversity of both prokaryotes and eukaryotes above, at, and below the photosynthetic fringe of twelve hot spring systems. Additionally, field measurements of dissolved oxygen, ferrous iron, and total sulfide were combined with laboratory analyses of sulfate, nitrate, total ammonium, dissolved inorganic carbon, dissolved methane, dissolved hydrogen, and dissolved carbon monoxide were used to calculate the available energy from 58 potential metabolisms. Results were ranked to identify those that yield the most energy according to the geochemical conditions of each system. Of the 46 samples taken across twelve systems, all showed the greatest energy yields using oxygen as the main electron acceptor, followed by nitrate. On the other hand, ammonium or ammonia, depending on pH, showed the greatest energy yields as an electron donor, followed by H2S or HS-. While some sequenced taxa reflect potential biotic participants in the sulfur cycle of these hot spring systems, many sample locations that yield the most energy from ammonium/ammonia oxidation have low relative abundances of known ammonium/ammonia oxidizers, indicating potentially untapped sources of chemotrophic energy or perhaps poorly understood metabolic capabilities of cultured chemotrophs.
ContributorsRomero, Joseph Thomas (Author) / Shock, Everett L (Thesis advisor) / Cadillo-Quiroz, Hinsby (Committee member) / Till, Christy B. (Committee member) / Arizona State University (Publisher)
Created2018
Description
Nitrous oxide (N2O) is a major contributor to the greenhouse effect and to stratospheric ozone depletion. In soils, nitrogen reduction is performed by biotic and abiotic processes, including microbial denitrification and chemical denitrification. Chemical denitrification, or chemodenitrification, is the abiotic step-wise reduction of nitrate (NO3-), nitrite (NO2-), or nitric oxide (NO) to N2O in anoxic environments, with high turnover rates particularly in acidic soils. Chemodenitrification was identified in various environments, but the mechanism is still not understood. In this study, the factors influencing abiotic reduction of NO2- to N2O in acidic tropical peat soil are examined. These factors include pH, organic matter content, and dissolved ferrous iron. Anoxic peat soil from sites located in the Peruvian Amazon was used for incubations. The results show that peat soil (pH ~4.5) appears to reduce NO2- more quickly in the presence of lower pH and higher Fe(II) concentrations. NO2- is completely reduced in excess Fe(II), and Fe(II) is completely oxidized in excess NO2-, providing evidence for the proposed mechanism of chemodenitrification. In addition, first order reaction rate constants kFe(II) and kNO2- were calculated using concentration measurements over 4 hours, to test for the hypothesized reaction rate relationships kFe(II): kFe(II) kFe(II)~NO2- > kFe(II)>NO2- and kNO2-: kFe(II)NO2-. The NO2- k values followed the anticipated pattern, although the Fe(II) k value data was inconclusive. Organic material may also play a role in NO2- reduction through chemodenitrification, and future experimentation will test this possibility. How and to what extent the pH and the concentrations of organic matter and Fe(II) affect the kinetic rate of chemodenitrification will lend insight into the N2O production potential of natural tropical peatlands.
ContributorsTylor, Kaitlyn Marie (Author) / Cadillo-Quiroz, Hinsby (Thesis director) / Day, Thomas (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Depletion of fossil fuel resources has led to the investigation of alternate feedstocks for and methods of chemical synthesis, in particular the use of E. coli biocatalysts to produce fine commodity chemicals from renewable glucose sources. Production of phenol, 2-phenylethanol, and styrene was investigated, in particular the limitation in yield and accumulation that results from high product toxicity. This paper examines two methods of product toxicity mitigation: the use of efflux pumps and the separation of pathways which produce less toxic intermediates. A library of 43 efflux pumps from various organisms were screened for their potential to confer resistance to phenol, 2-phenylethanol, and styrene on an E. coli host. A pump sourced from P. putida was found to allow for increased host growth in the presence of styrene as compared to a cell with no efflux pump. The separation of styrene producing pathway was also investigated. Cells capable of performing the first and latter halves of the synthesis were allowed to grow separately and later combined in order to capitalize on the relatively lower toxicity of the intermediate, trans-cinnamate. The styrene production and yield from this separated set of cultures was compared to that resulting from the growth of cells containing the full set of styrene synthesis genes. Results from this experiment were inconclusive.
ContributorsLallmamode, Noor Atiya Jabeen (Author) / Nielsen, David (Thesis director) / Cadillo-Quiroz, Hinsby (Committee member) / Barrett, The Honors College (Contributor) / Chemical Engineering Program (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Heliobacterium modesticaldum (H. modesticaldum) is an anaerobic photoheterotroph that can fix nitrogen (N2) and produce molecular hydrogen (H2). Recently, the Redding and Jones labs created a microbial photoelectrosynthesis cell that utilized these properties to produce molecular hydrogen using electrons provided by a cathode via a chemical mediator. Although this light-driven creation of fuel within a microbial electrochemical cell was the first of its kind, its production rate of hydrogen was low. It was hypothesized that the injection of electrons into H. modesticaldum was a rate-limiting step in H2 production. Within the H. modesticaldum genome, there is a gene (HM1_0653) that encodes a multi-heme cytochrome c that may be directly involved in this step. From past transcriptomic experiments, this gene is known to be very poorly expressed in H. modesticaldum. Our hypothesis was that increasing its expression with a strong promoter could result in faster electron transfer, and thus, increased H2 production in the photoelectrosynthesis cell. In order to test this hypothesis, different promoters that could lead to high expression in H. modesticaldum were included with a copy of HM1_0653 in various plasmid constructs that were first cloned into E. coli before being conjugated with H. modesticaldum. Cloning in E. coli was possible with the newly derived transformation system and by reducing the copy-number of the vector system. When overexpressed in E. coli, the protein appeared to be expressed, but its purification proved to be difficult. Moreover, conjugation with H. modesticaldum was not achieved. Our results are consistent with the idea that high level overexpression in H. modesticaldum was toxic. An inducible promoter may circumvent these issues and prove more successful in future experiments.
ContributorsSmith, Chelsea Elizabeth (Author) / Redding, Kevin (Thesis director) / Cadillo-Quiroz, Hinsby (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05