Matching Items (34)
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
The biological carbon pump in the ocean is initiated by the photosynthetic fixation of atmospheric carbon dioxide into particulate or dissolved organic carbon by phytoplankton. A fraction of this organic matter sinks to depth mainly in the form of microaggregates (5-60 μm) and visible macroaggregates. These aggregates are composed of cells, minerals, and other sources of organic carbon. Exopolymeric substances (EPS) are exudated by heterotrophic bacteria and phytoplankton and may form transparent exopolymeric particles (TEP) that act as a glue-like matrix for marine aggregates. Heterotrophic bacteria have been found to influence the aggregation of phytoplankton and in some cases result in an increase in TEP production, but it is unclear if marine heterotrophic bacteria can produce TEP and how they contribute to aggregation. Pseudoalteromonas carrageenovora, Vibrio thalassae, and Marinobacter adhaerens HP15 are heterotrophic marine bacteria that were found associated with sinking particles in an oligotrophic gyre station in the subtropical North Atlantic. These bacteria were grown in axenic cultures to determine growth, TEP production, and aggregation. They were also inoculated into roller tanks used to simulate open ocean conditions to determine their ability to form macroaggregates. Treatments with added kaolinite clay simulated aeolic dust input from the Sahara. M. adhaerens HP15 had the highest TEP concentration but the lowest cell-normalized TEP production at all growth stages compared to the other bacteria. Additionally, M. adhaerens HP15 also had the lowest microaggregate formation. The cell-normalized TEP production and microaggregate formation was not significantly different between P. carrageenovora and V. thalassae. All bacteria formed visible macroaggregates in roller tanks with clay addition and exhibited high sinking velocities (150-1200 m d-1) that are comparable to those of aggregates formed by large mineral ballasted phytoplankton. Microaggregates in the clay treatments declined during incubation, indicating that they aggregated to form the macroaggregates. The findings from this study show for the first time that heterotrophic bacteria can contribute to aggregation and the export of organic carbon to depth in the ocean.
ContributorsLivar, Britni (Author) / Neuer, Susanne (Thesis advisor) / Hartnett, Hilairy (Committee member) / Cadillo-Quiroz, Hinsby (Committee member) / Arizona State University (Publisher)
Created2022
Description
Immunotherapy uses the body’s immune system to find and terminate cancerous cells, and has revolutionized cancer treatment. However, in certain cancers, such as lung cancer, less than 50% of patients respond to treatment. This is in part due to the immunosuppressive tumor microenvironment, which is composed of factors that promote tumor growth and proliferation. Tumor cells create a highly immunosuppressive microenvironment by triggering the anti-inflammatory phenotype of myeloid immune cells, which largely consist of tumor-associated macrophages (TAMs). Anti-PD-1 and anti-PD-L1 immune checkpoint blockade therapy helps promote the T cell anti-tumor response by releasing the brakes on cytotoxic T-cells. However, it is unclear how TAMs respond to these immune checkpoint antibodies. Our lab hypothesizes that blockade of the PD-1/PD-L1 signaling pathway drives a pro-inflammatory macrophage phenotype. This hypothesis is supported by data generated in the B16F10 murine melanoma model, but it is unknown whether macrophage response to PD-L1 blockade is generalizable to other tumor contexts. Thus, the goal of the project is to determine the impact of immune checkpoint blockade on murine macrophages in the Lewis Lung Carcinoma (LLC) model. Using Flow Cytometry, macrophage phenotypes will be analyzed to confirm whether a pro- inflammatory or anti-tumor response is generated.
ContributorsKorpe, Sara (Author) / Cadillo-Quiroz, Hinsby (Thesis director) / Lancaster, Jessica (Committee member) / Barrett, The Honors College (Contributor) / Economics Program in CLAS (Contributor) / School of Life Sciences (Contributor)
Created2024-05
Description
Nitrous oxide (N2O) is an important greenhouse gas and an oxidant respired by a
diverse range of anaerobic microbes, but its sources and sinks are poorly understood. The overarching goal of my dissertation is to explore abiotic N2O formation and microbial N2O consumption across reducing environments of the early and modern Earth. By combining experiments as well as diffusion and atmospheric modeling, I present evidence that N2O production can be catalyzed on iron mineral surfaces that may have been present in shallow waters of the Archean ocean. Using photochemical models, I showed that tropospheric N2O concentrations close to modern ones (ppb range) were possible before O2 accumulated. In peatlands of the Amazon basin (modern Earth), unexpected abiotic activity became apparent under anoxic conditions. However, care has to be taken to adequately disentangle abiotic from biotic reactions. I identified significant sterilant-induced changes in Fe2+ and dissolved organic matter pools (determined by fluorescence spectroscopy). Among all chemical and physical sterilants tested, γ - irradiation showed the least effect on reactant pools. Targeting geochemically diverse peatlands across Central and South America, I present evidence that coupled abiotic and biotic cycling of N2O could be a widespread phenomenon. Using isotopic tracers in the field, I showed that abiotic N2O fluxes rival biotic ones under in-situ conditions. Moreover, once N2O is produced, it is rapidly consumed by N2O-reducing microbes. Using amplicon sequencing and metagenomics, I demonstrated that this surprising N2O sink potential is associated with diverse bacteria, including the recently discovered clade II that is present in high proportions at Amazonian sites based on nosZ quantities. Finally, to evaluate the impact of nitrogen oxides on methane production in peatlands, I characterized soil nitrite (NO2–) and N2O abundances along soil profiles. I complemented field analyses with molecular work by deploying amplicon-based 16S rRNA and mcrA sequencing. The diversity and activity of soil methanogens was affected by the presence of NO2– and N2O, suggesting that methane emissions could be influenced by N2O cycling dynamics. Overall, my work proposes a key role for N2O in Earth systems across time and a central position in tropical microbial ecosystems.
diverse range of anaerobic microbes, but its sources and sinks are poorly understood. The overarching goal of my dissertation is to explore abiotic N2O formation and microbial N2O consumption across reducing environments of the early and modern Earth. By combining experiments as well as diffusion and atmospheric modeling, I present evidence that N2O production can be catalyzed on iron mineral surfaces that may have been present in shallow waters of the Archean ocean. Using photochemical models, I showed that tropospheric N2O concentrations close to modern ones (ppb range) were possible before O2 accumulated. In peatlands of the Amazon basin (modern Earth), unexpected abiotic activity became apparent under anoxic conditions. However, care has to be taken to adequately disentangle abiotic from biotic reactions. I identified significant sterilant-induced changes in Fe2+ and dissolved organic matter pools (determined by fluorescence spectroscopy). Among all chemical and physical sterilants tested, γ - irradiation showed the least effect on reactant pools. Targeting geochemically diverse peatlands across Central and South America, I present evidence that coupled abiotic and biotic cycling of N2O could be a widespread phenomenon. Using isotopic tracers in the field, I showed that abiotic N2O fluxes rival biotic ones under in-situ conditions. Moreover, once N2O is produced, it is rapidly consumed by N2O-reducing microbes. Using amplicon sequencing and metagenomics, I demonstrated that this surprising N2O sink potential is associated with diverse bacteria, including the recently discovered clade II that is present in high proportions at Amazonian sites based on nosZ quantities. Finally, to evaluate the impact of nitrogen oxides on methane production in peatlands, I characterized soil nitrite (NO2–) and N2O abundances along soil profiles. I complemented field analyses with molecular work by deploying amplicon-based 16S rRNA and mcrA sequencing. The diversity and activity of soil methanogens was affected by the presence of NO2– and N2O, suggesting that methane emissions could be influenced by N2O cycling dynamics. Overall, my work proposes a key role for N2O in Earth systems across time and a central position in tropical microbial ecosystems.
ContributorsBuessecker, Steffen (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Hartnett, Hilairy E (Committee member) / Glass, Jennifer B (Committee member) / Hall, Sharon J (Committee member) / Arizona State University (Publisher)
Created2020
Description
Cyanobacteria and algae living inside carbonate rocks (endoliths) have long been considered major contributors to bioerosion. Some bore into carbonates actively (euendoliths); others simply inhabit pre-existing pore spaces (cryptoendoliths). While naturalistic descriptions based on morphological identification have traditionally driven the field, modern microbial ecology has shown that this approach is insufficient to assess microbial diversity or make functional inferences. I examined endolithic microbiomes using 16S rRNA genes and lipid-soluble photosynthetic pigments as biomarkers, with the goal of reassessing endolith diversity by contrasting traditional and molecular approaches. This led to the unexpected finding that in all 41 littoral carbonate microbiomes investigated around Isla de Mona (Puerto Rico) and Menorca (Spain) populations of anoxygenic phototrophic bacteria (APBs) in the phyla Chloroflexi and Proteobacteria, were abundant, even sometimes dominant over cyanobacteria. This was not only novel, but it suggested that APBs may have been previously misidentified as morphologically similar cyanobacteria, and opened questions about their potential role as euendoliths. To test the euendolithic role of photosynthetic microbes, I set a time-course experiment exposing virgin non-porous carbonate substrate in situ, under the hypothesis that only euendoliths would be able to initially colonize it. This revealed that endolithic microbiomes, similar in biomass to those of mature natural communities, developed within nine months of exposure. And yet, APB populations were still marginal after this period, suggesting that they are secondary colonizers and not euendolithic. However, elucidating colonization dynamics to a sufficiently accurate level of molecular identification among cyanobacteria required the development of a curated cyanobacterial 16S rRNA gene reference database and web tool, Cydrasil. I could then detect that the pioneer euendoliths were in a novel cyanobacterial clade (named UBC), immediately followed by cyanobacteria assignable to known euendoliths. However, as bioerosion proceeded, a diverse set of likely cryptoendolithic cyanobacteria colonized the resulting pore spaces, displacing euendoliths. Endolithic colonization dynamics are thus swift but complex, and involve functionally diverse agents, only some of which are euendoliths. My work contributes a phylogenetically sound, functionally more defined understanding of the carbonate endolithic microbiome, and more specifically, Cydrasil provides a user-friendly framework to routinely move beyond morphology-based cyanobacterial systematics.
ContributorsRoush, Daniel (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Anbar, Ariel (Committee member) / Cadillo-Quiroz, Hinsby (Committee member) / Cao, Huansheng (Committee member) / Arizona State University (Publisher)
Created2020
Description
Modern agriculture faces multiple challenges: it must produce more food for a growing global population, adopt more efficient and sustainable management strategies, and adapt to climate change. One potential component of a sustainable management strategy is the application of biochar to agricultural soils. Biochar is the carbon-rich product of biomass pyrolysis, which contains large proportions of aromatic compounds that influence its stability in soil. Concomitant with carbon sequestration, biochar has the potential to increase soil fertility through increasing soil pH, moisture and nutrient retention. Changes in the soil physical and chemical properties can result in shifts in the soil microbiome, which are the proximate drivers of soil processes. This dissertation aims to determine the compositional and functional changes in the soil microbial community in response to the addition of a low-volatile matter biochar. First, the impact of biochar on the bacterial community was investigated in two important agricultural soils (Oxisol and Mollisol) with contrasting fertility under two different cropping systems (conventional sweet corn and zero-tillage napiergrass) one month and one year after the initial addition. This study revealed that the effects of biochar on the bacterial community were most pronounced in the Oxisol under napiergrass cultivation, however soil type was the strongest determinant of the bacterial community. A follow-up study was conducted using shotgun metagenomics to probe the functional community of soil microcosms, which contained Oxisol soil under napiergrass two years after the initial addition of biochar. Biochar significantly increased total carbon in the soils but had little impact on other soil properties. Theses analyses showed that biochar-amended soil microcosms exhibited significant shifts in the functional community and key metabolic pathways related to carbon turnover and denitrification. Given the distinct alterations to the biochar-amended community, deoxyribose nucleic acid (DNA) stable isotope probing was used to target the active populations. These analyses revealed that biochar did not significantly shift the active community in soil microcosms. Overall, these results indicate that the impact of biochar on the active soil community is transient in nature. Yet, biochar may still be a promising strategy for long-term carbon sequestration in agricultural soils.
ContributorsYu, Julian (Author) / Penton, C. Ryan (Thesis advisor) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Hall, Sharon (Committee member) / Arizona State University (Publisher)
Created2020
Description
Methanogens anaerobically metabolize simple carbon compounds coupled with an electron donor and produce methane in a process known as methanogenesis. While their importance in anoxic ecosystems and their greenhouse gas emissions are known, less is known about their diverse members. This is in part due to limited culture-dependent studies as a consequence of the difficulty to culture and isolate them under laboratory conditions. Current methods in methanogen isolation require lengthy protocols, expensive equipment, can be easily contaminated, and even if a successful isolation is completed, traditional methods are biased towards only a few species of methanogens- leaving much of this community unsampled and thus unrepresented. New approaches in the isolation of methanogens need to be investigated in order to circumvent these obstacles. Here, I evaluated the effects of different strategies and alternative methods with the goal of increasing the diversity of recovered methanogens from Amazon peatlands as a study case. The results show that: a) through the use of different antibiotics the bacterial community makeup can be altered and lead to different methanogenic enrichments, some antibiotics reliably increase methanogenesis in all study sites, others only enhance it in some sites, while some have a low rate of methanogenesis enriching novel slow growers, b) the use of different substrates has less of an effect on methane production rates, however the complex substrate butyrate leads to consistent late stimulation, c) altering media components (reducing agent and overall geochemical background) for Amazon conditions would lead to a shorter time to isolation, d) and multiple methanogenic enrichments were achieved building on variable conditions and can lead to novel Amazon lineages. Molecular data is offering a more detailed view of bacteria and methanogens increasing or decreasing in response to treatments. Overall, it is shown that combining alternative approaches that manipulate interactions, metabolic substrate availability and culturing conditions could lead to more diverse isolation outputs from methanogenic cultures.
ContributorsAyers, Jillian (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Shi, Yixin (Committee member) / Trembath-Reichert, Elizabeth (Committee member) / Arizona State University (Publisher)
Created2021
Description
Prochlorococcus marinus (MED4), a genus of marine picocyanobacteria that proliferates in open oligotrophic ocean, is one of the most abundant photosynthetic microbes in the world, estimated to contribute up to 10% of the ocean’s primary production. The productivity of these microorganisms is controlled by macronutrient availability in the surface waters. The ratio of macronutrients in the ocean was defined, by Alfred Redfield, as an elemental ratio of 106C:16N:1P. However, the C:N:P ratio varies based on region, season, temperature and irradiance, as well as the composition of the primary producers. In oligotrophic gyres, these nutrient ratios are elevated from the Redfield stoichiometry, but whether this ratio exerts influence on the growth rate of the organism has not been investigated. Elemental stoichiometry of available nutrients can affect the aggregation of organic carbon and exportation of the particles to the ocean depths. The purpose of this study was to investigate the effects of nutrient limitation on aggregation and transparent exopolymeric particle (TEP) production which aids in aggregation. My findings suggested that nutrient limitation reduces TEP production and does not increase aggregate volume concentration. With continued warming, certain regions of the ocean will become more oligotrophic, which further decreases the nutrient supply available for Prochlorococcus. My research shows that this could lead to decreased exportation of organic carbon matter to the depths of the sea.
ContributorsRoy, Kevin Thomas (Author) / Neuer, Susanne (Thesis director) / Cadillo-Quiroz, Hinsby (Committee member) / Cruz, Bianca (Committee member) / Department of Psychology (Contributor) / School of Molecular Sciences (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Biological Soil Crusts (BSCs) are organosedimentary assemblages comprised of microbes and minerals in topsoil of terrestrial environments. BSCs strongly impact soil quality in dryland ecosystems (e.g., soil structure and nutrient yields) due to pioneer species such as Microcoleus vaginatus; phototrophs that produce filaments that bind the soil together, and support an array of heterotrophic microorganisms. These microorganisms in turn contribute to soil stability and biogeochemistry of BSCs. Non-cyanobacterial populations of BSCs are less well known than cyanobacterial populations. Therefore, we attempted to isolate a broad range of numerically significant and phylogenetically representative BSC aerobic heterotrophs. Combining simple pre-treatments (hydration of BSCs under dark and light) and isolation strategies (media with varying nutrient availability and protection from oxidative stress) we recovered 402 bacterial and one fungal isolate in axenic culture, which comprised 116 phylotypes (at 97% 16S rRNA gene sequence homology), 115 bacterial and one fungal. Each medium enriched a mostly distinct subset of phylotypes, and cultivated phylotypes varied due to the BSC pre-treatment. The fraction of the total phylotype diversity isolated, weighted by relative abundance in the community, was determined by the overlap between isolate sequences and OTUs reconstructed from metagenome or metatranscriptome reads. Together, more than 8% of relative abundance of OTUs in the metagenome was represented by our isolates, a cultivation efficiency much larger than typically expected from most soils. We conclude that simple cultivation procedures combined with specific pre-treatment of samples afford a significant reduction in the culturability gap, enabling physiological and metabolic assays that rely on ecologically relevant axenic cultures.
ContributorsNunes Da Rocha, Ulisses (Author) / Cadillo-Quiroz, Hinsby (Author) / Karaoz, Ulas (Author) / Rajeev, Lara (Author) / Klitgord, Niels (Author) / Dunn, Sean (Author) / Truong, Viet (Author) / Buenrostro, Mayra (Author) / Bowen, Benjamin P. (Author) / Garcia-Pichel, Ferran (Author) / Mukhopadhyay, Aindrila (Author) / Northen, Trent R. (Author) / Brodie, Eoin L. (Author) / College of Liberal Arts and Sciences (Contributor)
Created2015-03-19
Description
Northern peatland carbon cycling is under close observation and is critical to include in models projecting the future effects of climate change as these ecosystems represent a significant source of atmospheric methane (CH4). Changes in the in situ conditions, brought upon by the warming climate, could alter the rates of organic matter decomposition and accelerate the emissions of greenhouse, changing northern peatland’s status as a carbon sink. In order to develop a better understanding of the climate’s effect on the microbial community composition, carbon decomposition cascade, and flux of CH4 and CO2, anoxic soil microcosms were supplemented with either glucose or propionate to test the distinct intermediary metabolism of four northern peatland sites with statistically similar geochemistry that exist across a climate gradient. Lutose (LT) and Bog Lake (BL) consumed the supplemented glucose at the highest rates, 42.6 mg/L per day and 39.5 mg/L per day respectively. Chicago Bog (CB) and Daring Lake (DL) consumed the supplemented propionate at the highest rates, 5.26 mg/L per day and 4.34 mg/L per day respectively. BL microcosms showed low levels of methanogenesis as CH4 concentrations reached a maximum of 2.61 µmol/g dry soil in the treatments. In DL, the site with the highest production of CH4, the low abundance of hydrogenotrophic methanogens (Methanocellaceae and Methanoregulaceae) and relatively steady concentrations of acetate and formate could indicate that these are the more desired methanogenic substrates. These findings are indicative of the differences in metabolic potential found across these geochemically similar peatlands, lending to climate variables being a major driver in microbial community potential. To further characterize the intermediary metabolism and the effect of the climate gradient in these sites, future experimentations should incorporate 13C DNA-stable isotope probing data, establish a mass balance of the system, and incubate the microcosms at their respective in situ temperatures.
ContributorsBourquin, Brandon Phillip (Author) / Cadillo-Quiroz, Hinsby (Thesis director) / Marcus, Andrew (Committee member) / Sarno, Analissa F. (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05