Matching Items (34)
Description
The taxonomic and metabolic profile of the microbial community inhabiting a natural system is largely determined by the physical and geochemical properties of the system. However, the influences of parameters beyond temperature, pH and salinity have been poorly analyzed with few studies incorporating the comprehensive suite of physical and geochemical measurements required to fully investigate the complex interactions known to exist between biology and the environment. Further, the techniques used to classify the taxonomic and functional composition of a microbial community are fragmented and unwieldy, resulting in unnecessarily complex and often non-consilient results.
This dissertation integrates environmental metagenomes with extensive geochemical metadata for the development and application of multidimensional biogeochemical metrics. Analysis techniques including a Markov cluster-based evolutionary distance between whole communities, oligonucleotide signature-based taxonomic binning and principal component analysis of geochemical parameters allow for the determination of correlations between microbial community dynamics and environmental parameters. Together, these techniques allow for the taxonomic classification and functional analysis of the evolution of hot spring communities. Further, these techniques provide insight into specific geochemistry-biology interactions which enable targeted analyses of community taxonomic and functional diversity. Finally, analysis of synonymous substitution rates among physically separated microbial communities provides insights into microbial dispersion patterns and the roles of environmental geochemistry and community metabolism on DNA transfer among hot spring communities.
The data presented here confirms temperature and pH as the primary factors shaping the evolutionary trajectories of microbial communities. However, the integration of extensive geochemical metadata reveals new links between geochemical parameters and the distribution and functional diversification of communities. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial community functional composition and inter-community DNA transfer rates. Finally, the taxonomic classification and clustering techniques developed within this dissertation will facilitate future genomic and metagenomic studies through enhanced community profiling obtainable via Markov clustering, longer oligonucleotide signatures and insight into PCR primer biases.
This dissertation integrates environmental metagenomes with extensive geochemical metadata for the development and application of multidimensional biogeochemical metrics. Analysis techniques including a Markov cluster-based evolutionary distance between whole communities, oligonucleotide signature-based taxonomic binning and principal component analysis of geochemical parameters allow for the determination of correlations between microbial community dynamics and environmental parameters. Together, these techniques allow for the taxonomic classification and functional analysis of the evolution of hot spring communities. Further, these techniques provide insight into specific geochemistry-biology interactions which enable targeted analyses of community taxonomic and functional diversity. Finally, analysis of synonymous substitution rates among physically separated microbial communities provides insights into microbial dispersion patterns and the roles of environmental geochemistry and community metabolism on DNA transfer among hot spring communities.
The data presented here confirms temperature and pH as the primary factors shaping the evolutionary trajectories of microbial communities. However, the integration of extensive geochemical metadata reveals new links between geochemical parameters and the distribution and functional diversification of communities. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial community functional composition and inter-community DNA transfer rates. Finally, the taxonomic classification and clustering techniques developed within this dissertation will facilitate future genomic and metagenomic studies through enhanced community profiling obtainable via Markov clustering, longer oligonucleotide signatures and insight into PCR primer biases.
ContributorsAlsop, Eric Bennie (Author) / Raymond, Jason (Thesis advisor) / Anbar, Ariel (Committee member) / Farmer, Jack (Committee member) / Shock, Everett (Committee member) / Walker, Sarah (Committee member) / Arizona State University (Publisher)
Created2014
Description
Like individual organisms, complex social groups are able to maintain predictable trajectories of growth, from initial colony foundation to mature reproductively capable units. They do so while simultaneously responding flexibly to variation in nutrient availability and intake. Leafcutter ant colonies function as tri-trophic systems, in which the ants harvest vegetation to grow a fungus that, in turn, serves as food for the colony. Fungal growth rates and colony worker production are interdependent, regulated by nutritional and behavioral feedbacks. Fungal growth and quality are directly affected by worker foraging decisions, while worker production is, in turn, dependent on the amount and condition of the fungus. In this dissertation, I first characterized the growth relationship between the workers and the fungus of the desert leafcutter ant Acromyrmex versicolor during early stages of colony development, from colony foundation by groups of queens through the beginnings of exponential growth. I found that this relationship undergoes a period of slow growth and instability when workers first emerge, and then becomes allometrically positive. I then evaluated how mass and element ratios of resources collected by the ants are translated into fungus and worker population growth, and refuse, finding that colony digestive efficiency is comparable to digestive efficiencies of other herbivorous insects and ruminants. To test how colonies behaviorally respond to perturbations of the fungus garden, I quantified activity levels and task performance of workers in colonies with either supplemented or diminished fungus gardens, and found that colonies adjusted activity and task allocation in response to the fungus garden size. Finally, to identify possible forms of nutrient limitation, I measured how colony performance was affected by changes in the relative amounts of carbohydrates, protein, and phosphorus available in the resources used to grow the fungus garden. From this experiment, I concluded that colony growth is primarily carbohydrate-limited.
ContributorsClark, Rebecca, 1981- (Author) / Fewell, Jennifer H (Thesis advisor) / Mueller, Ulrich (Committee member) / Liebig, Juergen (Committee member) / Elser, James (Committee member) / Harrison, Jon (Committee member) / Arizona State University (Publisher)
Created2011
Description
Many studies over the past two decades examined the link between climate patterns and discharge, but few have attempted to study the effects of the El Niño Southern Oscillation (ENSO) on localized and watershed specific processes such as nutrient loading in the Southwestern United States. The Multivariate ENSO Index (MEI) is used to describe the state of the ENSO, with positive (negative) values referring to an El Niño condition (La Niña condition). This study examined the connection between the MEI and precipitation, discharge, and total nitrogen (TN) and total phosphorus (TP) concentrations in the Upper Salt River Watershed in Arizona. Unrestricted regression models (UMs) and restricted regression models (RMs) were used to investigate the relationship between the discharges in Tonto Creek and the Salt River as functions of the magnitude of the MEI, precipitation, and season (winter/summer). The results suggest that in addition to precipitation, the MEI/season relationship is an important factor for predicting discharge. Additionally, high discharge events were associated with high magnitude ENSO events, both El Niño and La Niña. An UM including discharge and season, and a RM (restricting the seasonal factor to zero), were applied to TN and TP concentrations in the Salt River. Discharge and seasonality were significant factors describing the variability in TN in the Salt River while discharge alone was the significant factor describing TP. TN and TP in Roosevelt Lake were evaluated as functions of both discharge and MEI. Some significant correlations were found but internal nutrient cycling as well as seasonal stratification of the water column of the lake likely masks the true relationships. Based on these results, the MEI is a useful predictor of discharge, as well as nutrient loading in the Salt River Watershed through the Salt River and Tonto Creek. A predictive model investigating the effect of ENSO on nutrient loading through discharge can illustrate the effects of large scale climate patterns on smaller systems.
ContributorsSversvold, Darren (Author) / Neuer, Susanne (Thesis advisor) / Elser, James (Committee member) / Fenichel, Eli (Committee member) / Arizona State University (Publisher)
Created2012
Description
Land management practices such as domestic animal grazing can alter plant communities via changes in soil structure and chemistry, species composition, and plant nutrient content. These changes can affect the abundance and quality of plants consumed by insect herbivores with consequent changes in population dynamics. These population changes can translate to massive crop damage and pest control costs. My dissertation focused on Oedaleus asiaticus, a dominant Asian locust, and had three main objectives. First, I identified morphological, physiological, and behavioral characteristics of the migratory ("brown") and non-migratory ("green") phenotypes. I found that brown morphs had longer wings, larger thoraxes and higher metabolic rates compared to green morphs, suggesting that developmental plasticity allows greater migratory capacity in the brown morph of this locust. Second, I tested the hypothesis of a causal link between livestock overgrazing and an increase in migratory swarms of O. asiaticus. Current paradigms generally assume that increased plant nitrogen (N) should enhance herbivore performance by relieving protein-limitation, increasing herbivorous insect populations. I showed, in contrast to this scenario, that host plant N-enrichment and high protein artificial diets decreased the size and viability of O. asiaticus. Plant N content was lowest and locust abundance highest in heavily livestock-grazed fields where soils were N-depleted, likely due to enhanced erosion and leaching. These results suggest that heavy livestock grazing promotes outbreaks of this locust by reducing plant protein content. Third, I tested for the influence of dietary imbalance, in conjunction with high population density, on migratory plasticity. While high population density has clearly been shown to induce the migratory morph in several locusts, the effect of diet has been unclear. I found that locusts reared at high population density and fed unfertilized plants (i.e. high quality plants for O. asiaticus) had the greatest migratory capacity, and maintained a high percent of brown locusts. These results did not support the hypothesis that poor-quality resources increased expression of migratory phenotypes. This highlights a need to develop new theoretical frameworks for predicting how environmental factors will regulate migratory plasticity in locusts and perhaps other insects.
ContributorsCease, Arianne (Author) / Harrison, Jon (Thesis advisor) / Elser, James (Thesis advisor) / DeNardo, Dale (Committee member) / Quinlan, Michael (Committee member) / Sabo, John (Committee member) / Arizona State University (Publisher)
Created2012
Description
The greatest barrier to understanding how life interacts with its environment is the complexity in which biology operates. In this work, I present experimental designs, analysis methods, and visualization techniques to overcome the challenges of deciphering complex biological datasets. First, I examine an iron limitation transcriptome of Synechocystis sp. PCC 6803 using a new methodology. Until now, iron limitation in experiments of Synechocystis sp. PCC 6803 gene expression has been achieved through media chelation. Notably, chelation also reduces the bioavailability of other metals, whereas naturally occurring low iron settings likely result from a lack of iron influx and not as a result of chelation. The overall metabolic trends of previous studies are well-characterized but within those trends is significant variability in single gene expression responses. I compare previous transcriptomics analyses with our protocol that limits the addition of bioavailable iron to growth media to identify consistent gene expression signals resulting from iron limitation. Second, I describe a novel method of improving the reliability of centroid-linkage clustering results. The size and complexity of modern sequencing datasets often prohibit constructing distance matrices, which prevents the use of many common clustering algorithms. Centroid-linkage circumvents the need for a distance matrix, but has the adverse effect of producing input-order dependent results. In this chapter, I describe a method of cluster edge counting across iterated centroid-linkage results and reconstructing aggregate clusters from a ranked edge list without a distance matrix and input-order dependence. Finally, I introduce dendritic heat maps, a new figure type that visualizes heat map responses through expanding and contracting sequence clustering specificities. Heat maps are useful for comparing data across a range of possible states. However, data binning is sensitive to clustering cutoffs which are often arbitrarily introduced by researchers and can substantially change the heat map response of any single data point. With an understanding of how the architectural elements of dendrograms and heat maps affect data visualization, I have integrated their salient features to create a figure type aimed at viewing multiple levels of clustering cutoffs, allowing researchers to better understand the effects of environment on metabolism or phylogenetic lineages.
ContributorsKellom, Matthew (Author) / Raymond, Jason (Thesis advisor) / Anbar, Ariel (Committee member) / Elser, James (Committee member) / Shock, Everett (Committee member) / Walker, Sarah (Committee member) / Arizona State University (Publisher)
Created2017
Description
“The Long Alchemy of Becoming: Aqua es Vida” is a short, artistic film depicting the history of the Universe shown through the microcosm of the Mexican town, Cuatro Ciénegas, in the state of Coahuila. The film takes the viewer from the start of the universe to what scientists believe will be its end, via a poem written by Dr. James Elser. “The Long Alchemy of Becoming: Aqua es Vida” starts with the Big Bang, through the formation of matter, stars, planets, including Earth. From there, the viewer witnesses how life evolved illustrated via scenes in the ciénegas (‘marsh’ in Spanish) found in Cuatro Ciénegas, Coahuila, Mexico. The film explores how life expanded out from water, producing plants and animals, including humans. Then, modern life in Cuatro Ciénegas is shown, including the modern agricultural practices that are threatening to destroy the ciénegas that sustain long histories of microbial evolution. The film concludes with the end mankind and the eventual destruction of Earth by the dying sun. Cuatro Ciénegas is a biologically and ecologically significant location, because its pools and marshes are home to many endemic species, including stromatolites, which are very rare, bio-chemical living structures. This film is part of a National Science Foundation grant, and reflects the extensive scientific research efforts in and around Cuatro Ciénegas and its unique pools.
ContributorsDavis, Samantha Kristen (Author) / Elser, James (Thesis director) / Lloyd, Samantha (Committee member) / Barrett, The Honors College (Contributor) / Walter Cronkite School of Journalism and Mass Communication (Contributor)
Created2015-05
Description
Many studies have shown that as the calcium carbonate precipitates, it sequesters phosphate. Although the geochemical interactions between phosphate and calcium carbonate are known, only a few studies have considered calcium carbonate deposition's effect on stream ecology. Further, those studies considering decomposition have produced conflicting results. In this study, nutrient-diffusing cups with organic substrata were used to determine the nutrient limitation of decomposers in the travertine streams in the Huachuca Mountains. After processing a subset of the experiments, only one site (in Huachuca Canyon) from the four study streams was significantly nutrient-limited (NP co-limitation).
ContributorsNevarez, Nicole Michelle (Author) / Elser, James (Thesis director) / Sabo, John (Committee member) / Corman, Jessica (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2013-05
Description
It is well known that deficiencies in key chemical elements (such as phosphorus, P) can reduce animal growth; however, recent empirical data have shown that high levels of dietary nutrients can also reduce animal growth. In ecological stoichiometry, this phenomenon is known as the "stoichiometric knife edge," but its underlying mechanisms are not well-known. Previous work has suggested that the crustacean zooplankter Daphnia reduces its feeding rates on phosphorus-rich food, causing low growth due to insufficient C (energy) intake. To test for this mechanism, feeding rates of Daphnia magna on algae (Scenedesmus acutus) differing in C:P ratio (P content) were determined. Overall, there was a significant difference among all treatments for feeding rate (p < 0.05) with generally higher feeding rates on P-rich algae. These data indicate that both high and low food C:P ratio do affect Daphnia feeding rate but are in contradiction with previous work that showed that P-rich food led to strong reductions in feeding rate. Additional experiments are needed to gain further insights.
ContributorsSchimpp, Sarah Ann (Author) / Elser, James (Thesis director) / Neuer, Susanne (Committee member) / Peace, Angela (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Sustainability (Contributor)
Created2014-05
Description
Microzooplankton, mainly heterotrophic unicellular eukaryotes (protists), play an important role in the cycling of nutrients and carbon in the sunlit (euphotic) zone of the world’s oceans. Few studies have investigated the microzooplankton communities in oligotrophic (low-nutrient) oceans, such as the Sargasso Sea. In this study, I investigate the seasonal and interannual dynamics of the heterotrophic protists, particularly the nanoflagellate, dinoflagellate, and ciliate communities, at the Bermuda Atlantic Time Series site and surrounding areas in the Sargasso Sea. In addition, I test the hypotheses that the community is controlled though bottom-up and top-down processes. To evaluate the bottom-up hypothesis, that the protists are controlled by prey availability, I test whether the protist abundance co-varies with the abundance of potential prey groups. Predation experiments with zooplankton were conducted and analyzed to test top-down control on the protists. I found distinguishable trends in biomass of the different protist groups between years and seasons. Nanoflagellates and dinoflagellates had higher biomass during the summer (28 ± 5 mgC/m2 and 44 ± 21 mgC/m2) than during the winter (17 ± 8 mgC/m2 and 30 ± 11 mgC/m2). Ciliates displayed the opposite trend with a higher average biomass in the winter (15 ± 9 mgC/m2) than in summer (5 ± 2 mgC/m2). In testing my bottom-up hypothesis, I found weak but significant positive grazer/prey relationships that indicate that nanoflagellates graze on picophytoplankton in winter and on the pico-cyanobacterium Prochlorococcus in summer. I found evidence that ciliates graze on Synechococcus in winter. I found weak but significant negative correlation between dinoflagellates and Prochlorococcus in summer. The predation experiments testing the top-down hypothesis did not show a clear top-down control, yet other studies in the region carried out during our investigation period support predation of the protists by the zooplankton. Overall, my results suggest a combination of bottom-up and top-down controls on these heterotrophic protists, however, further investigation is necessary to reveal the detailed trophic dynamics of these communities.
ContributorsWolverton, Megan (Author) / Neuer, Susanne (Thesis advisor) / Hartnett, Hillary (Committee member) / Elser, James (Committee member) / Arizona State University (Publisher)
Created2016
Description
Amazonia, inhabited and investigated for millennia, continues to astonish scientists with its cultural and natural diversity. Although Amazonia is rapidly changing, its vast and varied landscape still contains a complex natural pharmacopeia. The Amazonian tribes have accrued valuable environmental and geological knowledge that can be studied. This dissertation demonstrates that Indigenous Knowledge considered alongside Western Science can enhance our understanding of the relationship of people to geological materials and hydrological resources, and reveal mineral medicines with practical applications.
I used methods from anthropology and geology to explore the geological knowledge of the Uitoto, a tribe of the Colombian Amazon. The Uitoto use two metaphors to describe Earth systems: 1. the earth is a body, and 2. the Amazon is a tree. I found that they classify surface-water systems according to observable characteristics and use mineral clays to treat various maladies. I argue that Uitoto knowledge about Amazonian mineral resources and surface water is practical, empirically–based and, in many cases, more nuanced than mainstream scientific knowledge.
I studied the mode of action of a natural antibacterial clay from the Colombian Amazon (AMZ) to discover whether the Uitoto’s claims about the clay’s medicinal values was verifiable using the methods of Western Science. Natural antibacterial clays can inhibit the growth of human pathogens. Methods from microbiology and geochemistry were combined to evaluate the mineral-microbe interactions that inhibit growth of model Gram-negative (Escherichia coli) and Gram-positive (Bacillus subtilis) bacteria. The AMZ antibacterial clay contains 45 % kaolinites and 30 % smectites. Its high surface area maintains an acidic environment (pH 4.5) and releases high concentrations of aluminum. Aluminum accumulates in the outer membrane of E. coli by binding to phospholipids. Furthermore, the membrane’s permeability increases due to synergistic effects between aluminum and transition metals released from the AMZ (i.e. Fe, Cu). The changes in the membrane may compromise its function as a barrier. Understanding the antibacterial mechanism of AMZ is key for its safe use as a natural product. These findings can help us harness the capabilities of antibacterial clays more efficiently.
Lastly, I integrated the results of this work in place-based, cross-cultural educational materials tailored for the tribal schools in the Colombian Amazon. The design of the units was informed by principles of curriculum design and successful pedagogic approaches for Native American students. The purpose of these educational materials is to return the results of research, enhance learning and participation of indigenous peoples in geosciences, and respond to the multicultural and plurilingual educational needs in countries such as Colombia.
I used methods from anthropology and geology to explore the geological knowledge of the Uitoto, a tribe of the Colombian Amazon. The Uitoto use two metaphors to describe Earth systems: 1. the earth is a body, and 2. the Amazon is a tree. I found that they classify surface-water systems according to observable characteristics and use mineral clays to treat various maladies. I argue that Uitoto knowledge about Amazonian mineral resources and surface water is practical, empirically–based and, in many cases, more nuanced than mainstream scientific knowledge.
I studied the mode of action of a natural antibacterial clay from the Colombian Amazon (AMZ) to discover whether the Uitoto’s claims about the clay’s medicinal values was verifiable using the methods of Western Science. Natural antibacterial clays can inhibit the growth of human pathogens. Methods from microbiology and geochemistry were combined to evaluate the mineral-microbe interactions that inhibit growth of model Gram-negative (Escherichia coli) and Gram-positive (Bacillus subtilis) bacteria. The AMZ antibacterial clay contains 45 % kaolinites and 30 % smectites. Its high surface area maintains an acidic environment (pH 4.5) and releases high concentrations of aluminum. Aluminum accumulates in the outer membrane of E. coli by binding to phospholipids. Furthermore, the membrane’s permeability increases due to synergistic effects between aluminum and transition metals released from the AMZ (i.e. Fe, Cu). The changes in the membrane may compromise its function as a barrier. Understanding the antibacterial mechanism of AMZ is key for its safe use as a natural product. These findings can help us harness the capabilities of antibacterial clays more efficiently.
Lastly, I integrated the results of this work in place-based, cross-cultural educational materials tailored for the tribal schools in the Colombian Amazon. The design of the units was informed by principles of curriculum design and successful pedagogic approaches for Native American students. The purpose of these educational materials is to return the results of research, enhance learning and participation of indigenous peoples in geosciences, and respond to the multicultural and plurilingual educational needs in countries such as Colombia.
ContributorsLondoño Arias, Sandra Carolina (Author) / Williams, Lynda B (Thesis advisor) / Semken, Steven (Thesis advisor) / Brandt, Elizabeth A. (Committee member) / Hartnett, Hilairy H (Committee member) / Raymond, Jason (Committee member) / Arizona State University (Publisher)
Created2016