Matching Items (88)
Description
There is an estimated five trillion pieces of plastic in the global ocean, with 4.8 to 12.7 million metric tons entering the ocean annually. Much of the plastic in the ocean is in the form of microplastics, or plastic particles <5mm in size. Microplastics enter the marine environment as primary or secondary microplastics; primary microplastics are pre-manufactured micro-sized particles, such as microbeads used in cosmetics, while secondary microplastics form from the degradation of larger plastic objects, such water bottles. Once in the ocean, plastics are readily colonized by a consortium of prokaryotic and eukaryotic organisms, which form dense biofilms on the plastic; this biofilm is termed the “plastisphere”. Despite growing concerns about the ecological impact of microplastics and their respective plastispheres on the marine environment, there is little consensus about the factors that shape the plastisphere on environmentally relevant secondary microplastics. The goal of my dissertation is to comprehensively analyze the role of plastic polymer type, incubation time, and geographic location on shaping plastisphere communities attached to secondary microplastics. I investigated the plastisphere of six chemically distinct plastic polymer types obtained from common household consumer products that were incubated in the coastal Caribbean (Bocas del Toro, Panama) and coastal Pacific (San Diego, CA) oceans. Genotyping using 16S and 18S rRNA gene amplification and next-generation Illumina sequencing was employed to identify bacterial and eukaryotic communities on the polymer surfaces. Statistical analyses show that there were no polymer-specific assemblages for prokaryotes or eukaryotes, but rather a microbial core community that was shared among plastic types. I also found that rare hydrocarbon degrading bacteria may be specific to certain chemical properties of the microplastics. Statistical comparisons of the communities across both sites showed that prokaryotic plastispheres were shaped primarily by incubation time and geographic location. Finally, I assessed the impact of biofilms on microplastic degradation and deposition and conclude that biofilms enhance microplastic sinking of negatively buoyant particles and reduce microplastic degradation. The results of my dissertation increases understanding of the factors that shape the plastisphere and how these communities ultimately determine the fate of microplastics in the marine environment.
ContributorsDudek, Kassandra Lynn (Author) / Neuer, Susanne (Thesis advisor) / Polidoro, Beth (Committee member) / Garcia-Pichel, Ferran (Committee member) / Cao, Huansheng (Committee member) / Arizona State University (Publisher)
Created2021
Description
With the development and successful landing of the NASA Perseverance rover, there has been growing interest in identifying how evidence of ancient life may be preserved and recognized in the geologic record. Environments that enable fossilization of biological remains are termed, “taphonomic windows”, wherein signatures of past life may be detected. In this dissertation, I have sought to identify taphonomic windows in planetary-analog environments with an eye towards the exploration of Mars. In the first chapter, I describe how evidence of past microbial life may be preserved within serpentinizing systems. Owing to energetic rock-water reactions, these systems are known to host lithotrophic and organotrophic microbial communities. By investigating drill cores from the Samail Ophiolite in Oman, I report morphological and associated chemical biosignatures preserved in these systems as a result of subsurface carbonation. As serpentinites are known to occur on Mars and potentially other planetary bodies, these deposits potentially represent high-priority targets in the exploration for past microbial life. Next, I investigated samples from Atacama Desert, Chile, to understand how evidence of life may be preserved in ancient sediments formed originally in evaporative playa lakes. Here, I describe organic geochemical and morphological evidence of life preserved within sulfate-dominated evaporite rocks from the Jurassic-Cretaceous Tonel Formation and Oligocene San Pedro Formation. Because evaporative lakes are considered to have been potentially widespread on Mars, these deposits may represent additional key targets to search for evidence of past life. In the final chapter, I describe the fossilization potential of surficial carbonates by investigating Crystal Geyser, an active cold spring environment. Here, carbonate minerals precipitate rapidly in the presence of photosynthetic microbial mat communities. I describe how potential biosignatures are initially captured by mineralization, including cell-like structures and microdigitate stromatolites. However, these morphological signatures quickly degrade owing to diagenetic dissolution and recrystallization reactions, as well as textural coarsening that homogenizes the carbonate fabric. Overall, my dissertation underscores the complexity of microbial fossilization and highlights chemically-precipitating environments that may serve as high-priority targets for astrobiological exploration.
ContributorsZaloumis, Jonathan (Author) / Farmer, Jack D (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Trembath-Reichert, Elizabeth (Committee member) / Ruff, Steven W (Committee member) / Shock, Everett L (Committee member) / Arizona State University (Publisher)
Created2021
Description
The study of organismal adaptations oftentimes focuses on specific, constant conditions, but environmental parameters are characterized by more or less marked levels of variability, rather than constancy. This is important in environments like soils where microbial activity follows pulses of water availability driven by precipitation. Nowhere are these pulses more variable and unpredictable than in arid soils. Pulses constitute stressful conditions for bacteria because they cause direct cellular damage that must be repaired and they force cells to toggle between dormancy and active physiological states, which is energetically taxing. I hypothesize that arid soil microorganisms are adapted to the variability in wet/dry cycles itself, as determined by the frequency and duration of hydration pulses. To test this, I subjected soil microbiomes from the Chihuahuan Desert to controlled incubations for a total common growth period of 60 hours, but separated into treatments in which the total active time was reached with hydration pulses of different length with intervening periods of desiccation, so as to isolate pulse length and frequency as the varying factors in the experiment. Using 16S rRNA amplicon data, I characterized changes in microbiome growth, diversity, and species composition, and tracked the individual responses to treatment intensity in the 447 most common bacterial species (phylotypes) in the soil. Considering knowledge of extremophile microbiology, I hypothesized that growth yield and diversity would decline with shorter pulses. I found that microbial diversity was indeed a direct function of pulse length, but surprisingly, total yield was an inverse function of it. Pulse regime treatments resulted in progressively more significant differences in community composition with increasing pulse length, as differently adapted phylotypes became more prominent. In fact, more than 30% of the most common bacterial phylotypes demonstrated statistically significant population growth responses to pulse length. Most responsive phylotypes were apparently best adapted to short pulse regimes (known in the literature as Nimble Responders or NIRs), while fewer did better under long pulse regimes (known as TORs or Torpid Responders). Examples of extreme NIRs and TORs could be found among bacteria from different phyla, indicating that these adaptations have occurred multiple times during evolution.
ContributorsKut, Patrick John (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Sala, Osvaldo (Committee member) / Zhu, Qiyun (Committee member) / Arizona State University (Publisher)
Created2023
Description
Priced Managed Lanes (MLs) have been increasingly advocated as one of the effective ways to mitigating congestion in recent years. This study explores a new and innovative pricing strategy for MLs called Travel Time Refund (TTR). The proposed TTR provides an additional option to paying drivers that insures their travel time by issuing a refund to the toll cost if they do not reach their destination within specified travel times due to accidents or other unforeseen circumstances. Perceived benefits of TTR include raised public acceptance towards priced MLs, utilization increase of HOV/HOT lanes, overall congestion mitigation, and additional funding for relevant transportation agencies. To gauge travelers’ interests of TTR and to analyse its possible impacts, a stated preference (SP) survey was performed. An exploratory and statistical analysis of the survey responses revealed negative interest towards HOT and TTR option in accordance with common wisdom and previous studies. However, it is found that travelers are less negative about TTR than HOT alone; supporting the idea, that TTR could make HOT facilities more appealing. The impact of travel time reliability and latent variables representing psychological constructs on travelers’ choices in response to this new pricing strategy was also analysed. The results indicate that along with travel time and reliability, the decision maker’s attitudes and the level of comprehension of the concept of HOT and TTR play a significant role in their choice making. While the refund option may be theoretically and analytically feasible, the practical implementation issues cannot be ignored. This study also provides a discussion of the potential implementation considerations that include information provision to connected and non-connected vehicles, distinction between toll-only and refund customers, measurement of actual travel time, refund calculation and processing and safety and human factors issues. As the market availability of Connected and Automated Vehicles (CAVs) is prognosticated by 2020, the potential impact of such technologies on effective demand management, especially on MLs is worth investigating. Simulation analysis was performed to evaluate the system performance of a hypothetical road network at varying market penetration of CAVs. The results indicate that Connected Vehicles (CVs) could potentially encourage and enhance the use of MLs.
ContributorsVadlamani, Sravani (Author) / Lou, Yingyan (Thesis advisor) / Pendyala, Ram (Committee member) / Zhou, Xuesong (Committee member) / Grimm, Kevin (Committee member) / Arizona State University (Publisher)
Created2018
Description
Biological soil crusts (biocrusts) are topsoil communities of organisms that contribute to soil fertility and erosion resistance in drylands. Anthropogenic disturbances can quickly damage these communities and their natural recovery can take decades. With the development of accelerated restoration strategies in mind, I studied physiological mechanisms controlling the establishment of cyanobacteria in biocrusts, since these photoautotrophs are not just the biocrust pioneer organisms, but also largely responsible for improving key soil attributes such as physical stability, nutrient content, water retention and albedo. I started by determining the cyanobacterial community composition of a variety of biocrust types from deserts in the Southwestern US. I then isolated a large number of cyanobacterial strains from these locations, pedigreed them based on their 16SrRNA gene sequences, and selective representatives that matched the most abundant cyanobacterial field populations. I then developed methodologies for large-scale growth of the selected isolates to produce location-specific and genetically autochthonous inoculum for restoration. I also developed and tested viable methodologies to physiologically harden this inoculum and improve its survival under harsh field conditions. My tests proved that in most cases good viability of the inoculum could be attained under field-like conditions. In parallel, I used molecular ecology approaches to show that the biocrust pioneer, Microcoleus vaginatus, shapes its surrounding heterotrophic microbiome, enriching for a compositionally-differentiated “cyanosphere” that concentrates the nitrogen-fixing function. I proposed that a mutualism based on carbon for nitrogen exchange between M. vaginatus and its cyanosphere creates a consortium that constitutes the true pioneer community enabling the colonization of nitrogen-poor, bare soils. Using the right mixture of photosynthetic and diazotrophic cultures will thus likely help in soil restoration. Additionally, using physiological assays and molecular meta-analyses, I demonstrated that the largest contributors to N2-fixation in late successional biocrusts (three genera of heterocystous cyanobacteria) partition their niche along temperature gradients, and that this can explain their geographic patterns of dominance within biocrusts worldwide. This finding can improve restoration strategies by incorporating climate-matched physiological types in inoculum formulations. In all, this dissertation resulted in the establishment of a comprehensive "cyanobacterial biocrust nursery", that includes a culture collection containing 101 strains, isolation and cultivation methods, inoculum design strategies as well as field conditioning protocols. It constitutes a new interdisciplinary application of microbiology in restoration ecology.
ContributorsGiraldo Silva, Ana Maria (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Barger, Nichole N (Committee member) / Bowker, Mathew A (Committee member) / Sala, Osvaldo (Committee member) / Arizona State University (Publisher)
Created2019
Description
Euendolithic cyanobacteria have the remarkable ability to actively excavate and grow within certain minerals. Their activity leads to increased erosion of marine and terrestrial carbonates, negatively affecting coral reef and bivalve ecology. Despite their environmental relevance, the boring mechanism has remained elusive and paradoxical, in that cyanobacteria alkalinize their surroundings, typically leading to carbonate precipitation, not dissolution. Thus, euendoliths must rely on unique adaptations to bore. Recent work using the filamentous model euendolith Mastigocoleus testarum strain BC008 indicated that excavation relied on transcellular calcium transport mediated by P-type ATPases, but the phenomenon remained unclear. Here I present evidence that excavation in M. testarum involves an unprecedented set of adaptations. Long-range calcium transport is achieved through the coordinated pumping of multiple cells, orchestrated by the localization of calcium ATPases in a repeating annular pattern, positioned at a single cell pole, adjacent to each cell septum along the filament. Additionally, specialized chlorotic cells that I named calcicytes, differentiate and accumulate calcium at concentrations more than 500 fold those of canonical cells, likely allowing for fast calcium flow at non-toxic concentrations through undifferentiated cells. I also show, using 13C stable isotope tracers and NanoSIMS imaging, that endolithic M. testarum derives most of its carbon from the mineral carbonates it dissolves, the first autotroph ever shown to fix mineral carbon, confirming the existence of a direct link between oxidized solid carbon pools and reduced organic pools in the biosphere. Finally, using genomic and transcriptomic approaches, I analyze gene expression searching for additional adaptations related to the endolithic lifestyle. A large and diverse set of genes (24% of 6917 genes) were significantly differentially regulated while boring, including several master regulators and genes expectedly needed under this condition (such as transport, nutrient scavenging, oxidative stress, and calcium-binding protein genes). However, I also discovered the up-regulation of several puzzling gene sets involved in alternative carbon fixation pathways, anaerobic metabolism, and some related to photosynthesis and respiration. This transcriptomic data provides us with several new, readily testable hypotheses regarding adaptations to the endolithic lifestyle. In all, my data clearly show that boring organisms show extraordinarily interesting adaptations.
ContributorsGuida, Brandon Scott (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Chandler, Douglas (Committee member) / Bingham, Scott (Committee member) / Roberson, Robert (Committee member) / Arizona State University (Publisher)
Created2016
Description
Biological soil crusts (BSCs) dominate the soil surface of drylands in the western United States and possess properties thought to influence local hydrology. Little agreement exists, however, on the effects of BSCs on runoff, infiltration, and evaporative rates. This study aims to improve the predictive capability of an ecohydrology model in order to understand how BSCs affect the storage, retention, and infiltration of water into soils characteristic of the Colorado Plateau. A set of soil moisture measurements obtained at a climate manipulation experiment near Moab, Utah, are used for model development and testing. Over five years, different rainfall treatments over experimental plots resulted in the development of BSC cover with different properties that influence soil moisture differently. This study used numerical simulations to isolate the relative roles of different BSC properties on the hydrologic response at the plot-scale. On-site meteorological, soil texture and vegetation property datasets are utilized as inputs into a ecohydrology model, modified to include local processes: (1) temperature-dependent precipitation partitioning, snow accumulation and melt, (2) seasonally-variable potential evapotranspiration, (3) plant species-specific transpiration factors, and (4) a new module to account for the water balance of the BSC. Soil, BSC and vegetation parameters were determined from field measurements or through model calibration to the soil moisture observations using the Shuffled Complex Evolution algorithm. Model performance is assessed against five years of soil moisture measurements at each experimental site, representing a wide range of crust cover properties. Simulation experiments were then carried out using the calibrated ecohydrology model in which BSC parameters were varied according to the level of development of the BSC, as represented by the BSC roughness. These results indicate that BSCs act to both buffer against evaporative soil moisture losses by enhancing BSC moisture evaporation and significantly alter the rates of soil water infiltration by reducing moisture storage and increasing conductivity in the BSC. The simulation results for soil water infiltration, storage and retention across a wide range of meteorological events help explain the conflicting hydrologic outcomes present in the literature on BSCs. In addition, identifying how BSCs mediate infiltration and evaporation processes has implications for dryland ecosystem function in the western United States.
ContributorsWhitney, Kristen M (Author) / Vivoni, Enrique R (Thesis advisor) / Farmer, Jack D (Committee member) / Garcia-Pichel, Ferran (Committee member) / Arizona State University (Publisher)
Created2015
Description
This dissertation research is concerned with the study of two important traffic phenomena; merging and lane-specific traffic behavior. First, this research investigates merging traffic behavior through empirical analysis and evaluation of freeway merge ratios. Merges are important components of freeways and traffic behavior around them have a significant impact in the evolution and stability of congested traffic. At merges, drivers from conflicting traffic branches take turns to merge into a single stream at a rate referred to as the “merge ratio”. In this research, data from several freeway merges was used to evaluate existing macroscopic merge models and theoretical principles of merging behavior. Findings suggest that current merge ratio estimation methods can be insufficient to represent site-specific merge ratios, due to observed within-site variations and unaccounted effects of downstream merge geometry. To overcome these limitations, merge ratios were formulated based on their site-specific lane flow distribution (LFD), the proportion of flow in each freeway lane, for two types of merge geometries. Results demonstrate that the proposed methods are able to improve merge ratio estimates, reproduce within-site variations of merge ratio, and represent more effectively disproportionate redistribution of merging flow for merges where vehicles compete directly to merge due a downstream lane reduction.
Second, this research investigates lane-specific traffic behavior through empirical analysis and statistical modeling of lane flow distribution. Lane-specific traffic behavior is also an important component in evaluating freeway performance and has a significant impact in the mechanism of queue evolution, particularly around merges, and bottleneck discharge rate. In this research, site-specific linear LFD trends of three-lane congested freeways were investigated and modeled. A large-scale data collection process was implemented to systematically characterize the effects of several traffic and geometric features of freeways in the occurrence of between-site LFD variations. Also, an innovative three-stage modeling framework was used to model LFD behavior using multiple logistic regression to describe between-site LFD variations and Dirichlet regression to model recurrent combinations of linear LFD trends. This novel approach is able to represent both between and within site variations of LFD trends better, while accounting for the unit-sum constraint and distribution assumptions inherent of proportions data. Results revealed that proximity to freeway merges, a site’s level of congestion, and the presence of HOV lanes are significant factors that influence site-specific recurrent LFD behavior.
Findings from this work significantly improve the state-of-the-art knowledge on merging and lane-specific traffic behavior, which can help to improve traffic operations and reduce traffic congestion in freeways.
Second, this research investigates lane-specific traffic behavior through empirical analysis and statistical modeling of lane flow distribution. Lane-specific traffic behavior is also an important component in evaluating freeway performance and has a significant impact in the mechanism of queue evolution, particularly around merges, and bottleneck discharge rate. In this research, site-specific linear LFD trends of three-lane congested freeways were investigated and modeled. A large-scale data collection process was implemented to systematically characterize the effects of several traffic and geometric features of freeways in the occurrence of between-site LFD variations. Also, an innovative three-stage modeling framework was used to model LFD behavior using multiple logistic regression to describe between-site LFD variations and Dirichlet regression to model recurrent combinations of linear LFD trends. This novel approach is able to represent both between and within site variations of LFD trends better, while accounting for the unit-sum constraint and distribution assumptions inherent of proportions data. Results revealed that proximity to freeway merges, a site’s level of congestion, and the presence of HOV lanes are significant factors that influence site-specific recurrent LFD behavior.
Findings from this work significantly improve the state-of-the-art knowledge on merging and lane-specific traffic behavior, which can help to improve traffic operations and reduce traffic congestion in freeways.
ContributorsReina, Paulina (Author) / Ahn, Soyoung (Thesis advisor) / Pendyala, Ram (Committee member) / Kaloush, Kamil (Committee member) / Arizona State University (Publisher)
Created2015
Description
The ocean sequesters more than 25% of the carbon released by anthropogenic action every year, and oligotrophic oceans, such as the Sargasso Sea, are responsible for about 50% of the global carbon export. Pico- and nano-phytoplankton (cells < 5 µm), mostly unicellular eukaryotes (protists) and cyanobacteria, dominate the primary production in the Sargasso Sea; however, little is known about their contribution to the export of carbon into the deep ocean via sinking particles. The overall goal of this study is to examine the link between growth and grazing rates of pico- and nano-phytoplankton and the carbon export in the Sargasso Sea. I investigate three aspects: 1) how microzooplankton grazing and physical forcing affect taxon-specific primary productivity in this region, 2) how these microbial trophic dynamics impact their contribution to the export of particulate matter, and 3) how much pico-phytoplankton, specifically the pico-cyanobacteria Synechococcus and Prochlorococcus, contribute to the carbon export. I collected seawater samples within the sunlit (euphotic) zone, and sinking particles at 150 m depth using particle traps in the Sargasso Sea during the winter and summer seasons of 2011 and 2012. I conducted dilution experiments to determine the growth and grazing rates of the pico- and nano-phytoplankton community, and used 454 pyrosequencing and quantitative Polymerase Chain Reaction to measure the relative and absolute contribution of these primary producers to the plankton community within the euphotic zone and in the sinking particles. I found that micrograzing controls taxon-specific primary production, and that microbial trophic dynamics impact directly the taxonomical composition of the sinking particles. For the first time, I was able to quantify clade-specific carbon export of pico-cyanobacteria and found that, despite their small size, these tiny primary producers are capable of sinking from the surface to the deeper oceans. However, their contribution to the carbon flux is often less than one tenth of their biomass contribution in the euphotic zone. Our study provides a comprehensive approach to better understand the role of pico- and nano-phytoplankton in the carbon cycle of oligotrophic oceans, and a baseline to study changes in the carbon export in future warmer oceans.
ContributorsDe Martini, Francesca (Author) / Neuer, Susanne (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Hartnett, Hilairy (Committee member) / Lomas, Michael (Committee member) / Arizona State University (Publisher)
Created2016
Description
Alternative fuel vehicles (AFVs) have seen increased attention as a way to reduce reliance on petroleum for transportation, but adoption rates lag behind conventional vehicles. One crucial barrier to their proliferation is the lack of a convenient refueling infrastructure, and there is not a consensus on how to locate initial stations. Some approaches recommend placing stations near where early adopters live. An alternate group of methods places stations along busy travel routes that drivers from across the metropolitan area traverse each day. To assess which theoretical approach is most appropriate, drivers of compressed natural gas (CNG) vehicles in Southern California were surveyed at stations while they refueled. Through GIS analysis, results demonstrate that respondents refueled on the way between their origins and destinations ten times more often than they refueled near their home, when no station satisfied both criteria. Freeway interchanges, which carry high daily passing traffic volumes in metropolitan areas, can be appropriate locations for initial stations based on these results. Stations cannot actually be built directly at these interchange sites, so suitable locations on nearby street networks must be chosen. A network GIS method is developed to assess street network locations' ability to capture all traffic passing through 72 interchanges in greater Los Angeles, using deviation from a driver's shortest path as the metric to assess a candidate site's suitability. There is variation in the ability of these locations to capture passing traffic both within and across interchanges, but only 7% of sites near interchanges can conveniently capture all travel directions passing through the interchange, indicating that an ad hoc station location strategy is unlikely to succeed. Surveys were then conducted at CNG stations near freeway interchanges to assess how drivers perceive and access refueling stations in these environments. Through comparative analysis of drivers' perceptions of stations, consideration of their choice sets, and the observed frequency of the use of a freeway to both access and leave these stations, results indicate that initial AFV stations near freeway interchanges can play an important role in regional AFV infrastructure.
ContributorsKelley, Scott (Author) / Kuby, Michael (Thesis advisor) / Wentz, Elizabeth (Committee member) / Pendyala, Ram (Committee member) / Arizona State University (Publisher)
Created2015